# HG changeset patch
# User geert-vandeweyer
# Date 1395825862 14400
# Node ID 572397bbe05715ba93f7238b1016cc9eb202b383
# Parent  b2ad469e0ff97052735bd2f64671ffef9b6e32d0
Added Xmx10G setting to both varscan_somatic wrappers

diff -r b2ad469e0ff9 -r 572397bbe057 output.validation
--- a/output.validation	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,441 +0,0 @@
-##fileformat=VCFv4.1
-##source=VarScan2
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
-##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
-##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
-##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
-##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
-##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
-##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
-##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
-##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
-##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
-##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
-chr1	11190596	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
-chr1	11190597	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
-chr1	11190598	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:5,2,0,0
-chr1	11190599	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:6,1,0,0
-chr1	11190600	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:5,2,0,0
-chr1	11190601	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
-chr1	11190602	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:19:0:0%:13,6,0,0	0/0:.:11:8:0:0%:6,2,0,0
-chr1	11190603	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:14,6,0,0	0/0:.:11:11:0:0%:9,2,0,0
-chr1	11190604	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:13,7,0,0	0/0:.:13:12:0:0%:8,4,0,0
-chr1	11190605	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:13,7,0,0	0/0:.:13:10:0:0%:8,2,0,0
-chr1	11190606	.	G		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:20:0:0%:13,7,0,0	0/0:.:14:12:0:0%:8,4,0,0
-chr1	11190607	.	C		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:14:14:0:0%:9,5,0,0
-chr1	11190608	.	G		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:14:12:0:0%:7,5,0,0
-chr1	11190609	.	G		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:15:14:0:0%:9,5,0,0
-chr1	11190610	.	C		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190611	.	G		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:21:0:0%:13,8,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190612	.	A		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:13,8,0,0	0/0:.:15:13:0:0%:8,5,0,0
-chr1	11190613	.	T		.	PASS	DP=39;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:24:24:0:0%:13,11,0,0	0/0:.:15:14:0:0%:8,6,0,0
-chr1	11190614	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190615	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190616	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190617	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190618	.	T		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:12,12,0,0	0/0:.:15:13:0:0%:8,5,0,0
-chr1	11190619	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190620	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:15:15:0:0%:9,6,0,0
-chr1	11190621	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:14:0:0%:8,6,0,0
-chr1	11190622	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:16:14:0:0%:8,6,0,0
-chr1	11190623	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:12,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
-chr1	11190624	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
-chr1	11190625	.	G		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
-chr1	11190626	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
-chr1	11190627	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:11,12,0,0	0/0:.:17:16:0:0%:8,8,0,0
-chr1	11190628	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:16:0:0%:9,7,0,0
-chr1	11190629	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:16:0:0%:9,7,0,0
-chr1	11190630	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:16:16:0:0%:9,7,0,0
-chr1	11190631	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:8,7,0,0
-chr1	11190632	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:8,7,0,0
-chr1	11190633	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:24:0:0%:11,13,0,0	0/0:.:15:15:0:0%:8,7,0,0
-chr1	11190634	.	G		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:14,12,0,0	0/0:.:15:14:0:0%:8,6,0,0
-chr1	11190635	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:15:14:0:0%:7,7,0,0
-chr1	11190636	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:15:14:0:0%:7,7,0,0
-chr1	11190637	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
-chr1	11190638	.	T		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
-chr1	11190639	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
-chr1	11190640	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
-chr1	11190641	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
-chr1	11190642	.	C		.	PASS	DP=46;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:15,12,0,0	0/0:.:19:16:0:0%:9,7,0,0
-chr1	11190643	.	C		.	PASS	DP=50;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:29:29:0:0%:15,14,0,0	0/0:.:21:19:0:0%:10,9,0,0
-chr1	11190644	.	T		.	PASS	DP=51;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:30:0:0%:15,15,0,0	0/0:.:21:21:0:0%:12,9,0,0
-chr1	11190645	.	C		.	PASS	DP=52;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:29:0:0%:15,14,0,0	0/0:.:22:21:0:0%:12,9,0,0
-chr1	11190646	.	G	A	.	PASS	DP=53;SOMATIC;SS=2;SSC=13;GPV=1E0;SPV=4.429E-2	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/1:.:22:15:3:16.67%:9,6,1,2
-chr1	11190647	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:29:0:0%:13,16,0,0	0/0:.:22:20:0:0%:10,10,0,0
-chr1	11190648	.	T		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:20:0:0%:10,10,0,0
-chr1	11190649	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:22:0:0%:12,10,0,0
-chr1	11190650	.	T		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:22:0:0%:12,10,0,0
-chr1	11190651	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:30:0:0%:14,16,0,0	0/0:.:23:21:0:0%:11,10,0,0
-chr1	11190652	.	A		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:19:0:0%:10,9,0,0	0/0:.:19:17:0:0%:9,8,0,0
-chr1	11190653	.	C		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:17:0:0%:7,10,0,0	0/0:.:19:19:0:0%:9,10,0,0
-chr1	11190654	.	T		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:18:0:0%:8,10,0,0	0/0:.:19:17:0:0%:9,8,0,0
-chr1	11190655	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:7,8,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190656	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190657	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:14:13:0:0%:5,8,0,0
-chr1	11190658	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:7,8,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190659	.	C		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:14:13:0:0%:6,7,0,0
-chr1	11190660	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:17:0:0%:7,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190661	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190662	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:6,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190663	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:17:0:0%:7,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190664	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:15:0:0%:6,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
-chr1	11190665	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:8:0:0%:4,4,0,0
-chr1	11190666	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:12:0:0%:6,6,0,0
-chr1	11190667	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190668	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190669	.	T	A	.	str10	DP=32;SS=0;SSC=0;GPV=1E0;SPV=4.8148E-1	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:14:0:0%:5,9,0,0	1/1:.:15:12:1:7.69%:4,8,1,0
-chr1	11190670	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:14:0:0%:6,8,0,0	1/1:.:15:10:0:0%:5,5,0,0
-chr1	11190671	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:5,10,0,0	1/1:.:15:14:0:0%:6,8,0,0
-chr1	11190672	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190673	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:13:0:0%:5,8,0,0
-chr1	11190674	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:13:0:0%:7,6,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190675	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:5,10,0,0	1/1:.:15:14:0:0%:5,9,0,0
-chr1	11190676	.	A		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:6,9,0,0	1/1:.:15:14:0:0%:5,9,0,0
-chr1	11190677	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190678	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:13:0:0%:5,8,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190679	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:14:0:0%:6,8,0,0
-chr1	11190680	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190681	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
-chr1	11190682	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:13:0:0%:6,7,0,0
-chr1	11190683	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:14:0:0%:6,8,0,0
-chr1	11190684	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:14:0:0%:5,9,0,0	1/1:.:14:13:0:0%:4,9,0,0
-chr1	11190685	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:14:14:0:0%:5,9,0,0
-chr1	11190686	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:14:12:0:0%:5,7,0,0
-chr1	11190687	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:15:0:0%:6,9,0,0	1/1:.:12:11:0:0%:3,8,0,0
-chr1	11190688	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:15:0:0%:6,9,0,0	1/1:.:12:12:0:0%:4,8,0,0
-chr1	11190689	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:15:0:0%:6,9,0,0	1/1:.:12:11:0:0%:3,8,0,0
-chr1	11190690	.	T		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:14:0:0%:5,9,0,0	1/1:.:12:10:0:0%:4,6,0,0
-chr1	11190691	.	G		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:14:0:0%:5,9,0,0	1/1:.:12:12:0:0%:4,8,0,0
-chr1	11190692	.	G		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:5,8,0,0	1/1:.:12:11:0:0%:4,7,0,0
-chr1	11190693	.	C		.	PASS	DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:4,9,0,0	1/1:.:11:9:0:0%:3,6,0,0
-chr1	11190694	.	G		.	PASS	DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:4,9,0,0	1/1:.:11:9:0:0%:2,7,0,0
-chr1	11190695	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:12:12:0:0%:3,9,0,0	1/1:.:11:11:0:0%:3,8,0,0
-chr1	11319318	.	A		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:9:6:0:0%:4,2,0,0
-chr1	11319319	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:9:0:0%:4,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319320	.	G		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:7,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319321	.	G		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:8,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319322	.	T	G	.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=5E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:13:8:1:11.11%:5,3,0,1	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319323	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr1	11319324	.	A		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319325	.	C		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:13:0:0%:8,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319326	.	A		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319327	.	T		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:12:0:0%:7,5,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	11319328	.	A		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319329	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:8,6,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	11319330	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319331	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:9,5,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	11319332	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	11319333	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:13:0:0%:7,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319334	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	11319335	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45292432	.	C		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:31:0:0%:14,17,0,0	0/0:.:8:7:0:0%:2,5,0,0
-chr1	45292433	.	T		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:7:0:0%:2,5,0,0
-chr1	45292434	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:30:0:0%:15,15,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292435	.	G	C	.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=8.2051E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:31:1:3.12%:15,16,0,1	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45292436	.	C		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:30:0:0%:14,16,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45292437	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292438	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292439	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292440	.	A		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:28:0:0%:13,15,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292441	.	C		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:28:0:0%:12,16,0,0	0/0:.:8:8:0:0%:3,5,0,0
-chr1	45292442	.	T	A	.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=8.3333E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:29:1:3.33%:13,16,1,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293099	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293100	.	A		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:5,6,0,0	0/0:.:8:5:0:0%:2,3,0,0
-chr1	45293101	.	G		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:6:0:0%:2,4,0,0
-chr1	45293102	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293103	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293104	.	A		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293105	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:6,8,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293106	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:13:0:0%:6,7,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr1	45293107	.	T		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:6,8,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293108	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:6,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293109	.	C	C	.	str10	DP=23;SS=0;SSC=0;GPV=5.3885E-2;SPV=3.7799E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:15:13:2:13.33%:5,8,1,1	0/1:.:8:5:2:28.57%:3,2,0,2
-chr1	45293110	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:6,8,0,0	0/0:.:8:6:0:0%:2,4,0,0
-chr1	45293111	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
-chr1	45293112	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293113	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293114	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:5:0:0%:1,4,0,0
-chr1	45293115	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293116	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293117	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr1	45293118	.	T	T	.	PASS	DP=24;SS=0;SSC=0;GPV=5.4264E-2;SPV=4.3478E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:16:13:2:13.33%:4,9,1,1	0/1:.:8:6:2:25%:3,3,1,1
-chr1	45293119	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293120	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293121	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:13:0:0%:4,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293122	.	T		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:5,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr1	45293123	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:5,10,0,0	0/0:.:8:6:0:0%:4,2,0,0
-chr1	45293124	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:5,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr1	45293284	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:10,11,0,0	0/0:.:8:6:0:0%:3,3,0,0
-chr1	45293285	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:12,9,0,0	0/0:.:8:7:0:0%:5,2,0,0
-chr1	45293286	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:19:0:0%:8,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
-chr1	45293287	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:22:0:0%:11,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293288	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293289	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:21:0:0%:13,8,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293290	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
-chr1	45293291	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:22:0:0%:11,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr1	45293292	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:14,10,0,0	0/0:.:9:7:0:0%:4,3,0,0
-chr1	45293293	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:14,9,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	45293294	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:12,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
-chr1	45293295	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:14,9,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293296	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293297	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr1	45293298	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:14,10,0,0	0/0:.:9:7:0:0%:5,2,0,0
-chr1	45293299	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293300	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:22:0:0%:14,8,0,0	0/0:.:9:8:0:0%:5,3,0,0
-chr1	45293301	.	T		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:5,3,0,0
-chr1	45293302	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293303	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293304	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr1	45293305	.	T		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:12,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293306	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr1	45293307	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293308	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:8:0:0%:5,3,0,0
-chr1	45293309	.	G		.	PASS	DP=33;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:24:23:0:0%:13,10,0,0	0/0:.:9:9:0:0%:5,4,0,0
-chr1	45293310	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:22:0:0%:12,10,0,0	0/0:.:9:8:0:0%:5,3,0,0
-chr1	45293484	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:27,23,0,0	0/0:.:10:8:0:0%:5,3,0,0
-chr1	45293485	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293486	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293487	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293488	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:6:0:0%:5,1,0,0
-chr1	45293489	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293490	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293491	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293492	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293493	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:5:0:0%:5,0,0,0
-chr1	45293494	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293495	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293496	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:8:0:0%:5,3,0,0
-chr1	45293497	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:7:0:0%:4,3,0,0
-chr1	45293498	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:8:0:0%:5,3,0,0
-chr1	45293499	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:8:0:0%:4,4,0,0
-chr1	45293500	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293501	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:51:0:0%:27,24,0,0	0/0:.:10:8:0:0%:5,3,0,0
-chr1	45293502	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:8:0:0%:5,3,0,0
-chr1	45293503	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293504	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293505	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293506	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293507	.	A		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293508	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293509	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293510	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:27,25,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293511	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293512	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293513	.	A		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293514	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293515	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293516	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293517	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293518	.	A	G	.	PASS	DP=63;SOMATIC;SS=2;SSC=34;GPV=1E0;SPV=3.5255E-4	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/1:.:10:6:4:40%:3,3,2,2
-chr1	45293519	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293520	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293521	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293522	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293523	.	G	T	.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=8.3871E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:1:1.92%:25,26,0,1	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293524	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293525	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293526	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293527	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293528	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293529	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293530	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293531	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293532	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293533	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293534	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293535	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr1	45293536	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293537	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293538	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293539	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293540	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293541	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293542	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293543	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293544	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293545	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293546	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293547	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293548	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293549	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293550	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293551	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293552	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293553	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293554	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293555	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293556	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293557	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293558	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293559	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293560	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293561	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293562	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293563	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293564	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293565	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293566	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293567	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:26,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293568	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293569	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293570	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293571	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293572	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293573	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293574	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293575	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293576	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293577	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293578	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293579	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293580	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:48:0:0%:21,27,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293581	.	G		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:52:0:0%:26,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293582	.	G		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:52:0:0%:26,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293583	.	C		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:51:0:0%:25,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293584	.	A		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:50:0:0%:26,24,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293585	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293586	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293587	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293588	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293589	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293590	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
-chr1	45293591	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293592	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293593	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293594	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293595	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:25,24,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293596	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293597	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293598	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:48:0:0%:23,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293599	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:25,24,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293600	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293601	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293602	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293603	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293604	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
-chr1	45293605	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293606	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:8:0:0%:3,5,0,0
-chr1	45293607	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
-chr1	45293608	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293609	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293610	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293611	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293612	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293613	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:8:0:0%:3,5,0,0
-chr1	45293614	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293615	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293616	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr1	45293617	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
-chr1	45293618	.	G		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
-chr1	45293619	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293620	.	C		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
-chr1	45293621	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:6:0:0%:1,5,0,0
-chr1	45293622	.	C		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
-chr5	156750993	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr5	156750994	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156750995	.	A		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156750996	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156750997	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156750998	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156750999	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751000	.	C		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751001	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751006	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751007	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751008	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751009	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751010	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751011	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751012	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751013	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751014	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751015	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751016	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751017	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751018	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751019	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751020	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751021	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751022	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751023	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751024	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751025	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr5	156751026	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
-chr5	156751027	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751028	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751029	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751030	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751031	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751032	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751033	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751034	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751035	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751036	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751037	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751038	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751039	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751040	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751041	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751042	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751043	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751044	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751045	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751046	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751047	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751048	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
-chr5	156751049	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751050	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751051	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751052	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751053	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751054	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751055	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751056	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751057	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751058	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751059	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751060	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751061	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751062	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751063	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:6:0:0%:4,2,0,0
-chr5	156751064	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751065	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751066	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751067	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751068	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
-chr5	156751069	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751070	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751071	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751072	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751073	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751074	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751075	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156751076	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:5:0:0%:2,3,0,0
-chr5	156751077	.	T		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:17:0:0%:7,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
-chr5	156751078	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
-chr5	156788529	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:11:9:0:0%:4,5,0,0	0/0:.:9:7:0:0%:3,4,0,0
-chr5	156788530	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:9:6:0:0%:2,4,0,0
-chr5	156788531	.	C	CA	.	PASS	DP=21;SS=1;SSC=9;GPV=1.9541E-4;SPV=1.1491E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:11:7:4:36.36%:4,3,2,2	1/1:.:10:2:6:75%:1,1,3,3
-chr5	156788532	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
-chr5	156788533	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
-chr5	156788534	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:7:0:0%:5,2,0,0	0/0:.:10:3:0:0%:3,0,0,0
-chr5	156788535	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
-chr5	156788536	.	C		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr5	156788537	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:8:0:0%:4,4,0,0
-chr5	156788538	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788539	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:7,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788540	.	C		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:10:0:0%:5,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788541	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:6,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788542	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:11:10:0:0%:5,5,0,0	0/0:.:10:9:0:0%:5,4,0,0
-chr5	156788543	.	G		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788544	.	T		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788545	.	T		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788546	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
-chr5	156788547	.	C		.	PASS	DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:9:8:0:0%:4,4,0,0
-chr5	156788548	.	A		.	PASS	DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
diff -r b2ad469e0ff9 -r 572397bbe057 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="VarScan" version="2.3.5">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.5.jar</action>
-                <action type="move_file">
-                    <source>VarScan.v2.3.5.jar</source>
-                    <destination>$INSTALL_DIR/jars</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/output.validation
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/output.validation	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,441 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr1	11190596	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
+chr1	11190597	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
+chr1	11190598	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:5,2,0,0
+chr1	11190599	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:6,1,0,0
+chr1	11190600	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:7:0:0%:5,2,0,0
+chr1	11190601	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:13,7,0,0	0/0:.:8:8:0:0%:6,2,0,0
+chr1	11190602	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:19:0:0%:13,6,0,0	0/0:.:11:8:0:0%:6,2,0,0
+chr1	11190603	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:14,6,0,0	0/0:.:11:11:0:0%:9,2,0,0
+chr1	11190604	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:13,7,0,0	0/0:.:13:12:0:0%:8,4,0,0
+chr1	11190605	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:20:0:0%:13,7,0,0	0/0:.:13:10:0:0%:8,2,0,0
+chr1	11190606	.	G		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:20:0:0%:13,7,0,0	0/0:.:14:12:0:0%:8,4,0,0
+chr1	11190607	.	C		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:14:14:0:0%:9,5,0,0
+chr1	11190608	.	G		.	PASS	DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:14:12:0:0%:7,5,0,0
+chr1	11190609	.	G		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:15:14:0:0%:9,5,0,0
+chr1	11190610	.	C		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:13,9,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190611	.	G		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:21:0:0%:13,8,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190612	.	A		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:13,8,0,0	0/0:.:15:13:0:0%:8,5,0,0
+chr1	11190613	.	T		.	PASS	DP=39;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:24:24:0:0%:13,11,0,0	0/0:.:15:14:0:0%:8,6,0,0
+chr1	11190614	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190615	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190616	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190617	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190618	.	T		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:12,12,0,0	0/0:.:15:13:0:0%:8,5,0,0
+chr1	11190619	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190620	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:15:15:0:0%:9,6,0,0
+chr1	11190621	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:14:0:0%:8,6,0,0
+chr1	11190622	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:16:14:0:0%:8,6,0,0
+chr1	11190623	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:12,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
+chr1	11190624	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
+chr1	11190625	.	G		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
+chr1	11190626	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:17:0:0%:9,8,0,0
+chr1	11190627	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:11,12,0,0	0/0:.:17:16:0:0%:8,8,0,0
+chr1	11190628	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:16:0:0%:9,7,0,0
+chr1	11190629	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:17:16:0:0%:9,7,0,0
+chr1	11190630	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:16:16:0:0%:9,7,0,0
+chr1	11190631	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:8,7,0,0
+chr1	11190632	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:13,12,0,0	0/0:.:15:15:0:0%:8,7,0,0
+chr1	11190633	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:24:0:0%:11,13,0,0	0/0:.:15:15:0:0%:8,7,0,0
+chr1	11190634	.	G		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:14,12,0,0	0/0:.:15:14:0:0%:8,6,0,0
+chr1	11190635	.	C		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:15:14:0:0%:7,7,0,0
+chr1	11190636	.	T		.	PASS	DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:15:14:0:0%:7,7,0,0
+chr1	11190637	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
+chr1	11190638	.	T		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
+chr1	11190639	.	C		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
+chr1	11190640	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:26:0:0%:13,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
+chr1	11190641	.	G		.	PASS	DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:14,13,0,0	0/0:.:14:14:0:0%:7,7,0,0
+chr1	11190642	.	C		.	PASS	DP=46;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:27:27:0:0%:15,12,0,0	0/0:.:19:16:0:0%:9,7,0,0
+chr1	11190643	.	C		.	PASS	DP=50;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:29:29:0:0%:15,14,0,0	0/0:.:21:19:0:0%:10,9,0,0
+chr1	11190644	.	T		.	PASS	DP=51;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:30:0:0%:15,15,0,0	0/0:.:21:21:0:0%:12,9,0,0
+chr1	11190645	.	C		.	PASS	DP=52;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:29:0:0%:15,14,0,0	0/0:.:22:21:0:0%:12,9,0,0
+chr1	11190646	.	G	A	.	PASS	DP=53;SOMATIC;SS=2;SSC=13;GPV=1E0;SPV=4.429E-2	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/1:.:22:15:3:16.67%:9,6,1,2
+chr1	11190647	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:29:0:0%:13,16,0,0	0/0:.:22:20:0:0%:10,10,0,0
+chr1	11190648	.	T		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:20:0:0%:10,10,0,0
+chr1	11190649	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:22:0:0%:12,10,0,0
+chr1	11190650	.	T		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:31:31:0:0%:15,16,0,0	0/0:.:22:22:0:0%:12,10,0,0
+chr1	11190651	.	C		.	PASS	DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:30:0:0%:14,16,0,0	0/0:.:23:21:0:0%:11,10,0,0
+chr1	11190652	.	A		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:21:19:0:0%:10,9,0,0	0/0:.:19:17:0:0%:9,8,0,0
+chr1	11190653	.	C		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:17:0:0%:7,10,0,0	0/0:.:19:19:0:0%:9,10,0,0
+chr1	11190654	.	T		.	PASS	DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:18:0:0%:8,10,0,0	0/0:.:19:17:0:0%:9,8,0,0
+chr1	11190655	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:7,8,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190656	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190657	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:14:13:0:0%:5,8,0,0
+chr1	11190658	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:7,8,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190659	.	C		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:14:13:0:0%:6,7,0,0
+chr1	11190660	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:17:0:0%:7,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190661	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190662	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:6,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190663	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:17:0:0%:7,10,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190664	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:15:0:0%:6,9,0,0	0/0:.:14:14:0:0%:6,8,0,0
+chr1	11190665	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:8:0:0%:4,4,0,0
+chr1	11190666	.	C		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:17:16:0:0%:7,9,0,0	0/0:.:14:12:0:0%:6,6,0,0
+chr1	11190667	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190668	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190669	.	T	A	.	str10	DP=32;SS=0;SSC=0;GPV=1E0;SPV=4.8148E-1	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:14:0:0%:5,9,0,0	1/1:.:15:12:1:7.69%:4,8,1,0
+chr1	11190670	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:14:0:0%:6,8,0,0	1/1:.:15:10:0:0%:5,5,0,0
+chr1	11190671	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:5,10,0,0	1/1:.:15:14:0:0%:6,8,0,0
+chr1	11190672	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190673	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:13:0:0%:5,8,0,0
+chr1	11190674	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:13:0:0%:7,6,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190675	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:5,10,0,0	1/1:.:15:14:0:0%:5,9,0,0
+chr1	11190676	.	A		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:15:0:0%:6,9,0,0	1/1:.:15:14:0:0%:5,9,0,0
+chr1	11190677	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190678	.	T		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:13:0:0%:5,8,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190679	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:17:17:0:0%:7,10,0,0	1/1:.:15:14:0:0%:6,8,0,0
+chr1	11190680	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190681	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:15:0:0%:6,9,0,0
+chr1	11190682	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:13:0:0%:6,7,0,0
+chr1	11190683	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:15:14:0:0%:6,8,0,0
+chr1	11190684	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:14:0:0%:5,9,0,0	1/1:.:14:13:0:0%:4,9,0,0
+chr1	11190685	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:14:14:0:0%:5,9,0,0
+chr1	11190686	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:16:0:0%:7,9,0,0	1/1:.:14:12:0:0%:5,7,0,0
+chr1	11190687	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:16:15:0:0%:6,9,0,0	1/1:.:12:11:0:0%:3,8,0,0
+chr1	11190688	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:15:0:0%:6,9,0,0	1/1:.:12:12:0:0%:4,8,0,0
+chr1	11190689	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:15:0:0%:6,9,0,0	1/1:.:12:11:0:0%:3,8,0,0
+chr1	11190690	.	T		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:15:14:0:0%:5,9,0,0	1/1:.:12:10:0:0%:4,6,0,0
+chr1	11190691	.	G		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:14:0:0%:5,9,0,0	1/1:.:12:12:0:0%:4,8,0,0
+chr1	11190692	.	G		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:5,8,0,0	1/1:.:12:11:0:0%:4,7,0,0
+chr1	11190693	.	C		.	PASS	DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:4,9,0,0	1/1:.:11:9:0:0%:3,6,0,0
+chr1	11190694	.	G		.	PASS	DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:14:13:0:0%:4,9,0,0	1/1:.:11:9:0:0%:2,7,0,0
+chr1	11190695	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:12:12:0:0%:3,9,0,0	1/1:.:11:11:0:0%:3,8,0,0
+chr1	11319318	.	A		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:9:6:0:0%:4,2,0,0
+chr1	11319319	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:9:0:0%:4,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319320	.	G		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:7,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319321	.	G		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:8,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319322	.	T	G	.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=5E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:13:8:1:11.11%:5,3,0,1	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319323	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr1	11319324	.	A		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319325	.	C		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:13:0:0%:8,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319326	.	A		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:9,5,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319327	.	T		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:12:0:0%:7,5,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	11319328	.	A		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319329	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:8,6,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	11319330	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319331	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:9,5,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	11319332	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	11319333	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:13:0:0%:7,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319334	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	11319335	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:9,6,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45292432	.	C		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:31:0:0%:14,17,0,0	0/0:.:8:7:0:0%:2,5,0,0
+chr1	45292433	.	T		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:7:0:0%:2,5,0,0
+chr1	45292434	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:30:0:0%:15,15,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292435	.	G	C	.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=8.2051E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:31:1:3.12%:15,16,0,1	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45292436	.	C		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:30:0:0%:14,16,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45292437	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292438	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292439	.	G		.	PASS	DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:32:32:0:0%:15,17,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292440	.	A		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:28:0:0%:13,15,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292441	.	C		.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:28:0:0%:12,16,0,0	0/0:.:8:8:0:0%:3,5,0,0
+chr1	45292442	.	T	A	.	PASS	DP=38;SS=0;SSC=0;GPV=1E0;SPV=8.3333E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:30:29:1:3.33%:13,16,1,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293099	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293100	.	A		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:5,6,0,0	0/0:.:8:5:0:0%:2,3,0,0
+chr1	45293101	.	G		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:6:0:0%:2,4,0,0
+chr1	45293102	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293103	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293104	.	A		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293105	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:6,8,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293106	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:13:0:0%:6,7,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr1	45293107	.	T		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:14:14:0:0%:6,8,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293108	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:6,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293109	.	C	C	.	str10	DP=23;SS=0;SSC=0;GPV=5.3885E-2;SPV=3.7799E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:15:13:2:13.33%:5,8,1,1	0/1:.:8:5:2:28.57%:3,2,0,2
+chr1	45293110	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:6,8,0,0	0/0:.:8:6:0:0%:2,4,0,0
+chr1	45293111	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
+chr1	45293112	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293113	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293114	.	T		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:5:0:0%:1,4,0,0
+chr1	45293115	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:6,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293116	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293117	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:16:0:0%:6,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr1	45293118	.	T	T	.	PASS	DP=24;SS=0;SSC=0;GPV=5.4264E-2;SPV=4.3478E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:16:13:2:13.33%:4,9,1,1	0/1:.:8:6:2:25%:3,3,1,1
+chr1	45293119	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293120	.	G		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:14:0:0%:5,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293121	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:13:0:0%:4,9,0,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293122	.	T		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:14:0:0%:5,9,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr1	45293123	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:5,10,0,0	0/0:.:8:6:0:0%:4,2,0,0
+chr1	45293124	.	G		.	PASS	DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:15:15:0:0%:5,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr1	45293284	.	T		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:10,11,0,0	0/0:.:8:6:0:0%:3,3,0,0
+chr1	45293285	.	G		.	PASS	DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:21:0:0%:12,9,0,0	0/0:.:8:7:0:0%:5,2,0,0
+chr1	45293286	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:19:0:0%:8,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
+chr1	45293287	.	C		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:22:0:0%:11,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293288	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293289	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:21:0:0%:13,8,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293290	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
+chr1	45293291	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:22:0:0%:11,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr1	45293292	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:14,10,0,0	0/0:.:9:7:0:0%:4,3,0,0
+chr1	45293293	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:14,9,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	45293294	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:12,11,0,0	0/0:.:9:7:0:0%:3,4,0,0
+chr1	45293295	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:14,9,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293296	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293297	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr1	45293298	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:14,10,0,0	0/0:.:9:7:0:0%:5,2,0,0
+chr1	45293299	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293300	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:22:0:0%:14,8,0,0	0/0:.:9:8:0:0%:5,3,0,0
+chr1	45293301	.	T		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:5,3,0,0
+chr1	45293302	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293303	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293304	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr1	45293305	.	T		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:23:0:0%:12,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293306	.	C		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr1	45293307	.	A		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:24:0:0%:13,11,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293308	.	G		.	PASS	DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:25:25:0:0%:14,11,0,0	0/0:.:9:8:0:0%:5,3,0,0
+chr1	45293309	.	G		.	PASS	DP=33;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:24:23:0:0%:13,10,0,0	0/0:.:9:9:0:0%:5,4,0,0
+chr1	45293310	.	G		.	PASS	DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:23:22:0:0%:12,10,0,0	0/0:.:9:8:0:0%:5,3,0,0
+chr1	45293484	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:27,23,0,0	0/0:.:10:8:0:0%:5,3,0,0
+chr1	45293485	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293486	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293487	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293488	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:6:0:0%:5,1,0,0
+chr1	45293489	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293490	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293491	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293492	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:27,25,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293493	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:5:0:0%:5,0,0,0
+chr1	45293494	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293495	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293496	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:27,26,0,0	0/0:.:10:8:0:0%:5,3,0,0
+chr1	45293497	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:7:0:0%:4,3,0,0
+chr1	45293498	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:8:0:0%:5,3,0,0
+chr1	45293499	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:8:0:0%:4,4,0,0
+chr1	45293500	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293501	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:51:0:0%:27,24,0,0	0/0:.:10:8:0:0%:5,3,0,0
+chr1	45293502	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:8:0:0%:5,3,0,0
+chr1	45293503	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293504	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293505	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293506	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293507	.	A		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293508	.	G		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293509	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293510	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:52:0:0%:27,25,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293511	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293512	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293513	.	A		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:54:0:0%:27,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293514	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293515	.	C		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293516	.	T		.	PASS	DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:54:53:0:0%:27,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293517	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293518	.	A	G	.	PASS	DP=63;SOMATIC;SS=2;SSC=34;GPV=1E0;SPV=3.5255E-4	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/1:.:10:6:4:40%:3,3,2,2
+chr1	45293519	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293520	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293521	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293522	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293523	.	G	T	.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=8.3871E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:1:1.92%:25,26,0,1	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293524	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293525	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293526	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293527	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293528	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293529	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293530	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293531	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293532	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293533	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293534	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293535	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr1	45293536	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293537	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293538	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293539	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293540	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293541	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293542	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293543	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293544	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293545	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293546	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293547	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293548	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293549	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293550	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293551	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293552	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293553	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293554	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293555	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293556	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293557	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293558	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293559	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293560	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293561	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293562	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:25,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293563	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293564	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293565	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:52:0:0%:26,26,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293566	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293567	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:26,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293568	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293569	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293570	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293571	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293572	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293573	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293574	.	T		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293575	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293576	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293577	.	A		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293578	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:51:0:0%:25,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293579	.	C		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:53:0:0%:26,27,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293580	.	G		.	PASS	DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:53:48:0:0%:21,27,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293581	.	G		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:52:0:0%:26,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293582	.	G		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:52:0:0%:26,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293583	.	C		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:51:0:0%:25,26,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293584	.	A		.	PASS	DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:50:0:0%:26,24,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293585	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293586	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293587	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293588	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293589	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293590	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
+chr1	45293591	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293592	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293593	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293594	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293595	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:25,24,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293596	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293597	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293598	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:48:0:0%:23,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293599	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:25,24,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293600	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293601	.	A		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293602	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293603	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293604	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
+chr1	45293605	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293606	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:8:0:0%:3,5,0,0
+chr1	45293607	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
+chr1	45293608	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293609	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293610	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293611	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293612	.	T		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293613	.	G		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:25,25,0,0	0/0:.:10:8:0:0%:3,5,0,0
+chr1	45293614	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293615	.	C		.	PASS	DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:49:0:0%:24,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293616	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr1	45293617	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
+chr1	45293618	.	G		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:5:0:0%:0,5,0,0
+chr1	45293619	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:46:0:0%:21,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293620	.	C		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:9:0:0%:4,5,0,0
+chr1	45293621	.	T		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:6:0:0%:1,5,0,0
+chr1	45293622	.	C		.	PASS	DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:22,25,0,0	0/0:.:10:10:0:0%:5,5,0,0
+chr5	156750993	.	T		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr5	156750994	.	G		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156750995	.	A		.	PASS	DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:22:22:0:0%:10,12,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156750996	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156750997	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156750998	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156750999	.	G		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751000	.	C		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751001	.	A		.	PASS	DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:19:19:0:0%:10,9,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751006	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751007	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751008	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751009	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751010	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751011	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751012	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751013	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751014	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751015	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751016	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751017	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751018	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751019	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751020	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751021	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751022	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751023	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751024	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751025	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr5	156751026	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:3,4,0,0
+chr5	156751027	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751028	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751029	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751030	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751031	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751032	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751033	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751034	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751035	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751036	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751037	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751038	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751039	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751040	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751041	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751042	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751043	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751044	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751045	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751046	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751047	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751048	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
+chr5	156751049	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751050	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751051	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751052	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751053	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751054	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751055	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751056	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751057	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751058	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:10,9,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751059	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751060	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751061	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751062	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751063	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:6:0:0%:4,2,0,0
+chr5	156751064	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751065	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751066	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751067	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751068	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:7:0:0%:4,3,0,0
+chr5	156751069	.	G		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751070	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751071	.	T		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751072	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751073	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:20:0:0%:10,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751074	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:19:0:0%:9,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751075	.	C		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156751076	.	A		.	PASS	DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:20:18:0:0%:8,10,0,0	0/0:.:8:5:0:0%:2,3,0,0
+chr5	156751077	.	T		.	PASS	DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:18:17:0:0%:7,10,0,0	0/0:.:8:6:0:0%:2,4,0,0
+chr5	156751078	.	C		.	PASS	DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:16:15:0:0%:5,10,0,0	0/0:.:8:8:0:0%:4,4,0,0
+chr5	156788529	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:11:9:0:0%:4,5,0,0	0/0:.:9:7:0:0%:3,4,0,0
+chr5	156788530	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:6,6,0,0	0/0:.:9:6:0:0%:2,4,0,0
+chr5	156788531	.	C	CA	.	PASS	DP=21;SS=1;SSC=9;GPV=1.9541E-4;SPV=1.1491E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:11:7:4:36.36%:4,3,2,2	1/1:.:10:2:6:75%:1,1,3,3
+chr5	156788532	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
+chr5	156788533	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
+chr5	156788534	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:7:0:0%:5,2,0,0	0/0:.:10:3:0:0%:3,0,0,0
+chr5	156788535	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:8:0:0%:5,3,0,0	0/0:.:10:4:0:0%:3,1,0,0
+chr5	156788536	.	C		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr5	156788537	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:8:0:0%:4,4,0,0
+chr5	156788538	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:12:0:0%:7,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788539	.	A		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:7,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788540	.	C		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:10:0:0%:5,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788541	.	G		.	PASS	DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:12:11:0:0%:6,5,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788542	.	T		.	PASS	DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:11:10:0:0%:5,5,0,0	0/0:.:10:9:0:0%:5,4,0,0
+chr5	156788543	.	G		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788544	.	T		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788545	.	T		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788546	.	C		.	PASS	DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:10:0:0%:6,4,0,0	0/0:.:10:10:0:0%:6,4,0,0
+chr5	156788547	.	C		.	PASS	DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:9:8:0:0%:4,4,0,0
+chr5	156788548	.	A		.	PASS	DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:10:9:0:0%:5,4,0,0	0/0:.:9:9:0:0%:5,4,0,0
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/tool_dependencies.xml	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="VarScan" version="2.3.5">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.5.jar</action>
+                <action type="move_file">
+                    <source>VarScan.v2.3.5.jar</source>
+                    <destination>$INSTALL_DIR/jars</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan.tgz
Binary file varscan/varscan.tgz has changed
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_mpileup.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_mpileup.pl	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,121 @@
+#!/usr/bin/perl
+
+use strict;
+use Cwd;
+
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+my $options ="";
+my $file="";
+my $command="";
+my $output="";
+my $working_dir = cwd();
+my $temp_vcf = "$working_dir/temp";
+my $log="";
+
+foreach my $input (@ARGV) 
+{
+	my @tmp = split "::", $input;
+	if($tmp[0] eq "COMMAND") 
+	{
+		$command = $tmp[1];
+	} 
+	elsif($tmp[0] eq "INPUT") 
+	{
+		$file = $tmp[1];
+	}
+	elsif($tmp[0] eq "OPTION") 
+	{
+		my @p = split(/\s+/,$tmp[1]);
+		if ($p[0] =~ m/variants|strand-filter|output-vcf/ && $p[1] == 0) {
+			next;
+		}
+
+		$options = "$options ${tmp[1]}";
+	}
+	elsif($tmp[0] eq "OUTPUT") 
+	{
+		$output = $tmp[1];
+	}
+	elsif($tmp[0] eq "LOG") 
+	{
+		$log = $tmp[1];
+	}
+	else 
+	{
+		die("Unknown Input: $input\n");
+	}
+}
+
+system ("$command $file $options 1>$temp_vcf 2>$log");
+
+vs2vcf($temp_vcf, $output);
+
+
+sub vs2vcf 
+{
+
+	#
+	# G l o b a l     v a r i a b l e s 
+	#
+	my $version = '0.1';
+
+	#
+	# Read in file
+	#
+	my $input = shift;
+	my $output = shift;
+	my $chr_ord = shift;
+	open(IN, $input) or die "Can't open $input': $!\n";
+	open(OUT, ">$output") or die "Can't create $output': $!\n";
+	my %output;
+
+	while ( <IN> )
+	{
+		if ( /^#/ )
+		{
+			print OUT;
+			next;
+		}
+		chomp;
+		my $line = $_;
+
+		my @flds = split ( "\t", $line );
+		my $ref = $flds[3];
+		my $alt = $flds[4];
+		#
+		# Deletion of bases
+		#
+		if ( $alt =~ /^\-/ )
+		{
+			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
+		}
+
+		#
+		# Insertion of bases
+		#
+		if ( $alt =~ /^\+/ )
+		{
+			$flds[4] = $ref.substr($alt,1);
+		}
+		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
+		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
+	}
+	close(IN);
+	# if chromosome order given return in sorted order
+	if(defined $chr_ord) 
+	{
+		for my $chrom (@{ $chr_ord }) 
+		{
+			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
+			{
+				print OUT $output{$chrom}{$pos};
+			}
+		}
+	}
+	close(OUT);
+}
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_mpileup.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_mpileup.xml	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,124 @@
+<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5">
+  <description>
+        mutation caller for targeted, exome, and whole-genome resequencing
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_mpileup.pl 
+	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" 
+  	"INPUT::$in_file"
+  	"OUTPUT::$output"
+  	"LOG::$log"
+	"OPTION::--min-coverage $min_coverage"
+	"OPTION::--min-reads2 $min_reads2"
+	"OPTION::--min-avg-qual $min_avg_qual"
+	"OPTION::--min-var-freq $min_var_freq"
+	"OPTION::--min-freq-for-hom $min_freq_for_hom"
+	"OPTION::--p-value $p_value"	
+	"OPTION::--strand-filter $strand_filter"	
+	"OPTION::--output-vcf 1"	
+	
+	#if ($vcf_sample_list):
+		"OPTION::--vcf-sample-list $vcf_sample_list"
+	#end if
+	"OPTION::--variants $variants"	
+	
+	
+  	
+  </command>
+
+  <inputs>
+  	
+	<param name="exe_command" type="select" label="Command" help="" optional="false">
+		<option value="mpileup2snp" >mpileup2snp</option>
+		<option value="mpileup2indel">mpileup2indel</option>
+		<option value="mpileup2cns">mpileup2cns</option>
+	</param>
+	<param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
+	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
+	<param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
+	<param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
+	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
+	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
+	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
+	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
+	<param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
+	<param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
+	
+	
+  </inputs>
+  <outputs>
+  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
+  	<data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup file - The SAMtools mpileup file
+ 
+
+**Parameters**
+
+::
+
+  commands
+	mpileup2snp		Identify SNPs from an mpileup file
+	mpileup2indel		Identify indels an mpileup file
+	mpileup2cns		Call consensus and variants from an mpileup file
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-reads2	
+  	Minimum supporting reads at a position to call variants [2]
+
+  min-avg-qual	
+  	Minimum base quality at a position to count a read [15]
+
+  min-var-freq	
+        Minimum variant allele frequency threshold [0.01]
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  
+  p-value
+  	Default p-value threshold for calling variants [99e-02]
+  
+  strand-filter
+  	Ignore variants with >90% support on one strand [1]
+  
+  output-vcf
+  	If set to 1, outputs in VCF format
+  
+  vcf-sample-list
+  	For VCF output, a list of sample names in order, one per line
+  
+  variants
+  	Report only variant (SNP/indel) positions [0]
+
+
+  
+  </help>
+</tool>
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_processSomatic.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_processSomatic.pl	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,223 @@
+#!/usr/bin/perl
+
+
+use strict;
+use Cwd;
+
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+my $options ="";
+my $command="";
+my $input="";
+#my $output="";
+my $working_dir = cwd();
+my $log = '';
+my %outfiles;
+foreach my $arg (@ARGV) 
+{
+	my @tmp = split "::", $arg;
+	if($tmp[0] eq "COMMAND") 
+	{
+		$command = $tmp[1];
+	} 
+	elsif($tmp[0] eq "INPUT")
+	{
+		$input = $tmp[1];
+	}
+	elsif($tmp[0] eq "OPTION") 
+	{
+		my @p = split(/\s+/,$tmp[1]);
+		$options = "$options ${tmp[1]}";
+	}
+	elsif($tmp[0] eq "OUTPUT") 
+	{
+		my @p = split(/\s+/,$tmp[1]);
+		$p[0] = substr($p[0],2);
+		$outfiles{$p[0]} = $p[1];
+	}
+	
+	elsif($tmp[0] eq "LOG")
+        {
+                $log = $tmp[1];
+        }
+	else 
+	{
+		die("Unknown Input: $input\n");
+	}
+}
+system("ln -s $input $working_dir/in.dat");
+
+
+
+## RUN
+$command = "$command $working_dir/in.dat $options > $log 2>&1";
+system($command);
+
+## if tabular files are kept, write them to galaxy-datafile
+if ($outfiles{'loh'} ne 'None') {
+	## 
+	system("cp '$working_dir/in.dat.LOH' '".$outfiles{'loh'}."'");
+	system("cp '$working_dir/in.dat.LOH.hc' '".$outfiles{'loh'}."'");
+	system("cp '$working_dir/in.dat.Germline' '".$outfiles{'germ'}."'");
+	system("cp '$working_dir/in.dat.Germline.hc' '".$outfiles{'germ_hc'}."'");
+	system("cp '$working_dir/in.dat.Somatic' '".$outfiles{'som'}."'");
+	system("cp '$working_dir/in.dat.Somatic.hc' '".$outfiles{'som_hc'}."'");
+}
+## if vcf files are kept, generate them, and write to galaxy-datafile
+if ($outfiles{'loh_hc_vcf'} ne 'None') {
+	tab2vcf($working_dir,'in.dat.LOH.hc',$outfiles{'loh_hc_vcf'});
+	tab2vcf($working_dir,'in.dat.Germline.hc',$outfiles{'germ_hc_vcf'});
+	tab2vcf($working_dir,'in.dat.Somatic.hc',$outfiles{'som_hc_vcf'});
+}
+exit;
+
+sub tab2vcf
+{
+	my $wd = shift;
+	my $in = shift;
+	my $out = shift;
+	open OUT, ">$out";
+	print OUT "##fileformat=VCFv4.1\n";
+	print OUT "##source=processSomatic\n";
+	print OUT '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">'."\n";
+	print OUT '##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (Germline,Somatic,LOH)">'."\n";
+	print OUT '##INFO=<ID=VPV,Number=1,Type=Float,Description="Variant P-value">'."\n";
+	print OUT '##INFO=<ID=SPV,Number=1,Type=Float,Description="Somatic Variant P-value">'."\n";
+	print OUT '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">'."\n";
+	print OUT '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'."\n";
+	print OUT '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">'."\n";
+	print OUT '##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">'."\n";
+	print OUT '##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">'."\n";
+	print OUT '##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">'."\n";
+	print OUT '##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">'."\n";
+	print OUT '#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR'."\n";
+	open IN, "$wd/$in";
+	my $head = <IN>;
+	while (<IN>) {
+		chomp;
+		my @p = split(/\t/,$_);
+		my $td = $p[4] + $p[5] + $p[8] + $p[9];
+		my $vpv = sprintf('%.3E',$p[13]);
+		my $spv = sprintf('%.3E',$p[14]);
+		my $info = "DP=$td;SS=$p[12];VPV=$vpv;SPV=$spv";
+		## gt normal string
+		my $gtnormal = '';
+		if ("$p[7]" eq "$p[2]") {
+			$gtnormal = "0/0";
+		}
+		elsif ("$p[7]" eq "$p[3]") {
+			$gtnormal = "1/1";
+		}
+		else {
+			$gtnormal = "0/1";
+		}
+		my $nsum = $p[4] + $p[5];
+		$gtnormal .= ":.:$nsum:$p[4]:$p[5]:$p[6]:$p[19],$p[20],$p[21],$p[22]";
+		## gt tumor string
+		my $gttumor = '';
+		if ("$p[11]" eq "$p[2]") {
+			$gttumor = "0/0";
+		}
+		elsif ("$p[11]" eq "$p[3]") {
+			$gttumor = "1/1";
+		}
+		else {
+			$gttumor = "0/1";
+		}
+		my $tsum = $p[8] + $p[9];
+		$gttumor .= ":.:$tsum:$p[8]:$p[9]:$p[10]:$p[15],$p[16],$p[17],$p[18]";
+
+		## outline 
+		my $line = "$p[0]\t$p[1]\t.\t$p[2]\t$p[3]\t.\tPASS\t$info\tGT:GQ:DP:RD:AD:FREQ:DP4\t$gtnormal\t$gttumor\n";
+		print OUT $line;
+	}
+	close IN;
+	close OUT;
+}
+sub vs2vcf 
+{
+
+	#
+	# G l o b a l     v a r i a b l e s 
+	#
+	my $version = '0.1';
+
+	#
+	# Read in file
+	#
+	my $input = shift;
+	my $output = shift;
+	my $chr_ord = shift;
+	open(IN, $input) or die "Can't open $input': $!\n";
+	open(OUT, ">$output") or die "Can't create $output': $!\n";
+	my %output;
+
+	while ( <IN> )
+	{
+		if ( /^#/ )
+		{
+			print OUT;
+			next;
+		}
+		chomp;
+		my $line = $_;
+
+		my @flds = split ( "\t", $line );
+		my $ref = $flds[3];
+		my $alt = $flds[4];
+		#
+		# Deletion of bases
+		#
+		if ( $alt =~ /^\-/ )
+		{
+			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
+		}
+
+		#
+		# Insertion of bases
+		#
+		if ( $alt =~ /^\+/ )
+		{
+			$flds[4] = $ref.substr($alt,1);
+		}
+		## insert dot for reference positions.
+		if ($flds[4] eq '') {
+			$flds[4] = '.';
+		}
+		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
+		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
+	}
+	close(IN);
+	# if chromosome order given return in sorted order
+	if(defined $chr_ord) 
+	{
+		for my $chrom (@{ $chr_ord }) 
+		{
+			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
+			{
+				print OUT $output{$chrom}{$pos};
+			}
+		}
+	}
+	close(OUT);
+}
+
+
+sub chromosome_order 
+{
+	my $input = shift;
+	# calculate flagstats
+	my $COMM = "samtools view -H $input | grep '^\@SQ'";
+	my @SQ = `$COMM`;
+	chomp @SQ;
+	for(my $i = 0; $i <= $#SQ; $i++) 
+	{
+		$SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/;
+	} 
+	return(@SQ);
+}
+
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_processSomatic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_processSomatic.xml	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,154 @@
+<tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5">
+  <description>
+        Extract HC calls from Somatic Caller
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_processSomatic.pl 
+  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic" 
+	"INPUT::$input"
+        "LOG::$log"
+  	
+	"OPTION::--min-tumor-freq $min_tumor_freq"
+	"OPTION::--max-normal-freq $max_normal_freq"
+	"OPTION::--p-value $p_value"
+	"OUTPUT::--loh $loh"
+	"OUTPUT::--loh_hc $loh_hc"
+	"OUTPUT::--germ $germ"
+	"OUTPUT::--germ_hc $germ_hc"
+	"OUTPUT::--som $som"
+	"OUTPUT::--som_hc $som_hc"
+	"OUTPUT::--som_hc_vcf $som_hc_vcf"
+	"OUTPUT::--germ_hc_vcf $germ_hc_vcf"
+	"OUTPUT::--loh_hc_vcf $loh_hc_vcf"
+	
+  </command>
+
+  <inputs>
+
+	<param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" />
+
+	<param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/>
+	<param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/>
+	<param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/>
+	<param name="outtype" type="select" label="Output Type:" default="1">
+		<option value="0">Native VarScan Tables</option>
+		<option value="1">VCF format (only High Confidence)</option>
+		<option value="2">Both</option>
+	</param>
+
+  </inputs>
+  <outputs>
+        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " />
+        <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " >
+		<filter>outtype != "1"</filter>
+	</data>
+	<data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)">
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)">
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" >
+		<filter>outtype != "1"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+	<data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" >
+		<filter>outtype != "0"</filter>
+	</data>
+
+
+	
+
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup normal file - The SAMtools mpileup file for normal
+  mpileup tumor file - The SAMtools mpileup file for tumor
+ 
+
+**Parameters**
+
+::
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-coverage-normal	
+  	Minimum coverage in normal to call somatic [8]
+  	
+  min-coverage-tumor	
+  	Minimum coverage in tumor to call somatic [6]
+  	
+  min-var-freq 
+  	Minimum variant frequency to call a heterozygote [0.10]  	  	
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  	
+  normal-purity 
+  	Estimated purity (non-tumor content) of normal sample [1.00]
+  	
+  tumor-purity
+  	Estimated purity (tumor content) of tumor sample [1.00]
+  
+  p-value
+  	Default p-value threshold for calling variants [0.99]
+  	
+  somatic-p-value
+  	P-value threshold to call a somatic site [0.05]  	
+  
+  strand-filter
+  	If set to 1, removes variants with >90% strand bias
+  	
+  validation 
+  	If set to 1, outputs all compared positions even if non-variant
+  
+  output-vcf
+  	If set to 1, outputs in VCF format [Default]
+
+
+  
+  </help>
+</tool>
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_somatic.native.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_somatic.native.xml	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,139 @@
+<tool id="varscan_somatic_native" name="VarScan Somatic (Native Output)" version="2.3.5">
+  <description>
+        somatic mutation caller for cancer genomics
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_somatic.pl 
+  	"COMMAND::java -Xmx10G -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" 
+  	"NORMAL::$normal" 
+  	"TUMOR::$tumor"
+	"TUMORBAM::$tumorbam"
+	"SNP::$snp"
+	"INDEL::$indel"
+        "LOG::$log"
+  	
+	"OPTION::--min-coverage $min_coverage"
+	"OPTION::--min-coverage-normal $min_coverage_normal"
+	"OPTION::--min-coverage-tumor $min_coverage_tumor"
+	
+	"OPTION::--min-var-freq $min_var_freq"
+	"OPTION::--min-freq-for-hom $min_freq_for_hom"
+	
+	"OPTION::--normal-purity $normal_purity"	
+	"OPTION::--tumor-purity $tumor_purity"		
+	
+	"OPTION::--p-value $p_value"	
+	"OPTION::--somatic-p-value $somatic_p_value"	
+
+	"OPTION::--strand-filter $strand_filter"	
+	"OPTION::--validation $validation"	
+	
+
+  	
+  </command>
+
+  <inputs>
+
+	<param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
+	<param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
+	<param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
+
+	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
+	<param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
+	<param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
+	
+	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
+	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
+	
+	<param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
+	<param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
+	
+
+	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
+	<param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
+
+	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
+	<param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
+	
+  </inputs>
+  <outputs>
+        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
+	<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP)" />
+	<data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL)" />
+	
+
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup normal file - The SAMtools mpileup file for normal
+  mpileup tumor file - The SAMtools mpileup file for tumor
+ 
+
+**Parameters**
+
+::
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-coverage-normal	
+  	Minimum coverage in normal to call somatic [8]
+  	
+  min-coverage-tumor	
+  	Minimum coverage in tumor to call somatic [6]
+  	
+  min-var-freq 
+  	Minimum variant frequency to call a heterozygote [0.10]  	  	
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  	
+  normal-purity 
+  	Estimated purity (non-tumor content) of normal sample [1.00]
+  	
+  tumor-purity
+  	Estimated purity (tumor content) of tumor sample [1.00]
+  
+  p-value
+  	Default p-value threshold for calling variants [0.99]
+  	
+  somatic-p-value
+  	P-value threshold to call a somatic site [0.05]  	
+  
+  strand-filter
+  	If set to 1, removes variants with >90% strand bias
+  	
+  validation 
+  	If set to 1, outputs all compared positions even if non-variant
+  
+  output-vcf
+  	If set to 1, outputs in VCF format [Default]
+
+
+  
+  </help>
+</tool>
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_somatic.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_somatic.pl	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,173 @@
+#!/usr/bin/perl
+
+
+use strict;
+use Cwd;
+
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+my $options ="";
+my $normal="";
+my $command="";
+my $tumor="";
+my $tumorbam = "";
+my $output="";
+my $snp="";
+my $indel="";
+my $working_dir = cwd();
+my $log = '';
+
+foreach my $input (@ARGV) 
+{
+	my @tmp = split "::", $input;
+	if($tmp[0] eq "COMMAND") 
+	{
+		$command = $tmp[1];
+	} 
+	elsif($tmp[0] eq "NORMAL") 
+	{
+		$normal = $tmp[1];
+	} 
+	elsif($tmp[0] eq "TUMOR") 
+	{
+		$tumor = $tmp[1];
+	}
+	elsif($tmp[0] eq "TUMORBAM")
+	{
+		$tumorbam = $tmp[1];
+	}
+	elsif($tmp[0] eq "OPTION") 
+	{
+		my @p = split(/\s+/,$tmp[1]);
+		if ($p[0] =~ m/validation|strand-filter|output-vcf/ && $p[1] == 0) {
+			next;
+		}
+		$options = "$options ${tmp[1]}";
+	}
+	elsif($tmp[0] eq "OUTPUT") 
+	{
+		$output = $tmp[1];
+	}
+	elsif($tmp[0] eq "SNP") 
+	{
+		$snp = $tmp[1];
+	}
+	elsif($tmp[0] eq "INDEL") 
+	{
+		$indel = $tmp[1];
+	}
+
+	elsif($tmp[0] eq "LOG")
+        {
+                $log = $tmp[1];
+        }
+	
+	else 
+	{
+		die("Unknown Input: $input\n");
+	}
+}
+
+## VCF OUTPUT 
+if ($output ne '') {
+	system ("$command $normal $tumor $options --output-snp $working_dir/out.snp --output-indel $working_dir/out.indel 2>$log");
+	my $indels = "$working_dir/out.indel.vcf";
+	my $snps = "$working_dir/out.snp.vcf";
+	
+	system("grep -v '^\#' $indels | grep -v '^chrom position' >> $snps");
+	my @chr_ord = chromosome_order($tumorbam);
+
+	vs2vcf($snps, $output,\@chr_ord);
+}
+## SNP/INDEL OUTPUT
+else {
+	system  ("$command $normal $tumor $options --output-snp $snp --output-indel $indel 2>$log");
+}
+
+sub vs2vcf 
+{
+
+	#
+	# G l o b a l     v a r i a b l e s 
+	#
+	my $version = '0.1';
+
+	#
+	# Read in file
+	#
+	my $input = shift;
+	my $output = shift;
+	my $chr_ord = shift;
+	open(IN, $input) or die "Can't open $input': $!\n";
+	open(OUT, ">$output") or die "Can't create $output': $!\n";
+	my %output;
+
+	while ( <IN> )
+	{
+		if ( /^#/ )
+		{
+			print OUT;
+			next;
+		}
+		chomp;
+		my $line = $_;
+
+		my @flds = split ( "\t", $line );
+		my $ref = $flds[3];
+		my $alt = $flds[4];
+		#
+		# Deletion of bases
+		#
+		if ( $alt =~ /^\-/ )
+		{
+			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
+		}
+
+		#
+		# Insertion of bases
+		#
+		if ( $alt =~ /^\+/ )
+		{
+			$flds[4] = $ref.substr($alt,1);
+		}
+		## insert dot for reference positions.
+		if ($flds[4] eq '') {
+			$flds[4] = '.';
+		}
+		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
+		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
+	}
+	close(IN);
+	# if chromosome order given return in sorted order
+	if(defined $chr_ord) 
+	{
+		for my $chrom (@{ $chr_ord }) 
+		{
+			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
+			{
+				print OUT $output{$chrom}{$pos};
+			}
+		}
+	}
+	close(OUT);
+}
+
+
+sub chromosome_order 
+{
+	my $input = shift;
+	# calculate flagstats
+	my $COMM = "samtools view -H $input | grep '^\@SQ'";
+	my @SQ = `$COMM`;
+	chomp @SQ;
+	for(my $i = 0; $i <= $#SQ; $i++) 
+	{
+		$SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/;
+	} 
+	return(@SQ);
+}
+
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan/varscan_somatic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan/varscan_somatic.xml	Wed Mar 26 05:24:22 2014 -0400
@@ -0,0 +1,140 @@
+<tool id="varscan_somatic_vcf" name="VarScan Somatic (VCF Output)" version="2.3.5">
+  <description>
+        somatic mutation caller for cancer genomics
+  </description>
+  <requirements>
+  	<requirement type="package" version="2.3.5">VarScan</requirement>
+  </requirements>
+  <command interpreter="perl">
+  	
+	varscan_somatic.pl 
+  	"COMMAND::java -Xmx10G -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" 
+  	"NORMAL::$normal" 
+  	"TUMOR::$tumor"
+	"TUMORBAM::$tumorbam"
+  	"OUTPUT::$output"
+        "LOG::$log"
+  	
+	"OPTION::--min-coverage $min_coverage"
+	"OPTION::--min-coverage-normal $min_coverage_normal"
+	"OPTION::--min-coverage-tumor $min_coverage_tumor"
+	
+	"OPTION::--min-var-freq $min_var_freq"
+	"OPTION::--min-freq-for-hom $min_freq_for_hom"
+	
+	"OPTION::--normal-purity $normal_purity"	
+	"OPTION::--tumor-purity $tumor_purity"		
+	
+	"OPTION::--p-value $p_value"	
+	"OPTION::--somatic-p-value $somatic_p_value"	
+
+	"OPTION::--strand-filter $strand_filter"	
+	"OPTION::--validation $validation"	
+	"OPTION::--output-vcf 1"	
+	
+
+  	
+  </command>
+
+  <inputs>
+
+	<param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
+	<param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
+	<param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
+
+	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
+	<param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
+	<param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
+	
+	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
+	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
+	
+	<param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
+	<param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
+	
+
+	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
+	<param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
+
+	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
+	<param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
+	
+  </inputs>
+  <outputs>
+  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
+        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
+	<!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
+	<data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
+	
+
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+::
+
+ VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
+
+    Germline variants (SNPs an dindels) in individual samples or pools of samples.
+    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
+    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
+    Somatic copy number alterations (CNAs) in tumor-normal exome data.
+
+
+**Input**
+
+::
+
+  mpileup normal file - The SAMtools mpileup file for normal
+  mpileup tumor file - The SAMtools mpileup file for tumor
+ 
+
+**Parameters**
+
+::
+
+  min-coverage	
+  	Minimum read depth at a position to make a call [8]
+
+  min-coverage-normal	
+  	Minimum coverage in normal to call somatic [8]
+  	
+  min-coverage-tumor	
+  	Minimum coverage in tumor to call somatic [6]
+  	
+  min-var-freq 
+  	Minimum variant frequency to call a heterozygote [0.10]  	  	
+
+  min-freq-for-hom
+  	Minimum frequency to call homozygote [0.75]
+  	
+  normal-purity 
+  	Estimated purity (non-tumor content) of normal sample [1.00]
+  	
+  tumor-purity
+  	Estimated purity (tumor content) of tumor sample [1.00]
+  
+  p-value
+  	Default p-value threshold for calling variants [0.99]
+  	
+  somatic-p-value
+  	P-value threshold to call a somatic site [0.05]  	
+  
+  strand-filter
+  	If set to 1, removes variants with >90% strand bias
+  	
+  validation 
+  	If set to 1, outputs all compared positions even if non-variant
+  
+  output-vcf
+  	If set to 1, outputs in VCF format [Default]
+
+
+  
+  </help>
+</tool>
+
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_mpileup.pl
--- a/varscan_mpileup.pl	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Cwd;
-
-die qq(
-Bad numbr of inputs
-
-) if(!@ARGV);
-
-my $options ="";
-my $file="";
-my $command="";
-my $output="";
-my $working_dir = cwd();
-my $temp_vcf = "$working_dir/temp";
-my $log="";
-
-foreach my $input (@ARGV) 
-{
-	my @tmp = split "::", $input;
-	if($tmp[0] eq "COMMAND") 
-	{
-		$command = $tmp[1];
-	} 
-	elsif($tmp[0] eq "INPUT") 
-	{
-		$file = $tmp[1];
-	}
-	elsif($tmp[0] eq "OPTION") 
-	{
-		my @p = split(/\s+/,$tmp[1]);
-		if ($p[0] =~ m/variants|strand-filter|output-vcf/ && $p[1] == 0) {
-			next;
-		}
-
-		$options = "$options ${tmp[1]}";
-	}
-	elsif($tmp[0] eq "OUTPUT") 
-	{
-		$output = $tmp[1];
-	}
-	elsif($tmp[0] eq "LOG") 
-	{
-		$log = $tmp[1];
-	}
-	else 
-	{
-		die("Unknown Input: $input\n");
-	}
-}
-
-system ("$command $file $options 1>$temp_vcf 2>$log");
-
-vs2vcf($temp_vcf, $output);
-
-
-sub vs2vcf 
-{
-
-	#
-	# G l o b a l     v a r i a b l e s 
-	#
-	my $version = '0.1';
-
-	#
-	# Read in file
-	#
-	my $input = shift;
-	my $output = shift;
-	my $chr_ord = shift;
-	open(IN, $input) or die "Can't open $input': $!\n";
-	open(OUT, ">$output") or die "Can't create $output': $!\n";
-	my %output;
-
-	while ( <IN> )
-	{
-		if ( /^#/ )
-		{
-			print OUT;
-			next;
-		}
-		chomp;
-		my $line = $_;
-
-		my @flds = split ( "\t", $line );
-		my $ref = $flds[3];
-		my $alt = $flds[4];
-		#
-		# Deletion of bases
-		#
-		if ( $alt =~ /^\-/ )
-		{
-			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
-		}
-
-		#
-		# Insertion of bases
-		#
-		if ( $alt =~ /^\+/ )
-		{
-			$flds[4] = $ref.substr($alt,1);
-		}
-		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
-		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
-	}
-	close(IN);
-	# if chromosome order given return in sorted order
-	if(defined $chr_ord) 
-	{
-		for my $chrom (@{ $chr_ord }) 
-		{
-			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
-			{
-				print OUT $output{$chrom}{$pos};
-			}
-		}
-	}
-	close(OUT);
-}
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_mpileup.xml
--- a/varscan_mpileup.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5">
-  <description>
-        mutation caller for targeted, exome, and whole-genome resequencing
-  </description>
-  <requirements>
-  	<requirement type="package" version="2.3.5">VarScan</requirement>
-  </requirements>
-  <command interpreter="perl">
-  	
-	varscan_mpileup.pl 
-	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" 
-  	"INPUT::$in_file"
-  	"OUTPUT::$output"
-  	"LOG::$log"
-	"OPTION::--min-coverage $min_coverage"
-	"OPTION::--min-reads2 $min_reads2"
-	"OPTION::--min-avg-qual $min_avg_qual"
-	"OPTION::--min-var-freq $min_var_freq"
-	"OPTION::--min-freq-for-hom $min_freq_for_hom"
-	"OPTION::--p-value $p_value"	
-	"OPTION::--strand-filter $strand_filter"	
-	"OPTION::--output-vcf 1"	
-	
-	#if ($vcf_sample_list):
-		"OPTION::--vcf-sample-list $vcf_sample_list"
-	#end if
-	"OPTION::--variants $variants"	
-	
-	
-  	
-  </command>
-
-  <inputs>
-  	
-	<param name="exe_command" type="select" label="Command" help="" optional="false">
-		<option value="mpileup2snp" >mpileup2snp</option>
-		<option value="mpileup2indel">mpileup2indel</option>
-		<option value="mpileup2cns">mpileup2cns</option>
-	</param>
-	<param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
-	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
-	<param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
-	<param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
-	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
-	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
-	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
-	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
-	<param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
-	<param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
-	
-	
-  </inputs>
-  <outputs>
-  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
-  	<data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
-  </outputs>
-  	
-  <help> 
-
-.. class:: infomark
-
-**What it does**
-
-::
-
- VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
-
-    Germline variants (SNPs an dindels) in individual samples or pools of samples.
-    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
-    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
-    Somatic copy number alterations (CNAs) in tumor-normal exome data.
-
-
-**Input**
-
-::
-
-  mpileup file - The SAMtools mpileup file
- 
-
-**Parameters**
-
-::
-
-  commands
-	mpileup2snp		Identify SNPs from an mpileup file
-	mpileup2indel		Identify indels an mpileup file
-	mpileup2cns		Call consensus and variants from an mpileup file
-
-  min-coverage	
-  	Minimum read depth at a position to make a call [8]
-
-  min-reads2	
-  	Minimum supporting reads at a position to call variants [2]
-
-  min-avg-qual	
-  	Minimum base quality at a position to count a read [15]
-
-  min-var-freq	
-        Minimum variant allele frequency threshold [0.01]
-
-  min-freq-for-hom
-  	Minimum frequency to call homozygote [0.75]
-  
-  p-value
-  	Default p-value threshold for calling variants [99e-02]
-  
-  strand-filter
-  	Ignore variants with >90% support on one strand [1]
-  
-  output-vcf
-  	If set to 1, outputs in VCF format
-  
-  vcf-sample-list
-  	For VCF output, a list of sample names in order, one per line
-  
-  variants
-  	Report only variant (SNP/indel) positions [0]
-
-
-  
-  </help>
-</tool>
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_processSomatic.pl
--- a/varscan_processSomatic.pl	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
-#!/usr/bin/perl
-
-
-use strict;
-use Cwd;
-
-die qq(
-Bad numbr of inputs
-
-) if(!@ARGV);
-
-my $options ="";
-my $command="";
-my $input="";
-#my $output="";
-my $working_dir = cwd();
-my $log = '';
-my %outfiles;
-foreach my $arg (@ARGV) 
-{
-	my @tmp = split "::", $arg;
-	if($tmp[0] eq "COMMAND") 
-	{
-		$command = $tmp[1];
-	} 
-	elsif($tmp[0] eq "INPUT")
-	{
-		$input = $tmp[1];
-	}
-	elsif($tmp[0] eq "OPTION") 
-	{
-		my @p = split(/\s+/,$tmp[1]);
-		$options = "$options ${tmp[1]}";
-	}
-	elsif($tmp[0] eq "OUTPUT") 
-	{
-		my @p = split(/\s+/,$tmp[1]);
-		$p[0] = substr($p[0],2);
-		$outfiles{$p[0]} = $p[1];
-	}
-	
-	elsif($tmp[0] eq "LOG")
-        {
-                $log = $tmp[1];
-        }
-	else 
-	{
-		die("Unknown Input: $input\n");
-	}
-}
-system("ln -s $input $working_dir/in.dat");
-
-
-
-## RUN
-$command = "$command $working_dir/in.dat $options > $log 2>&1";
-system($command);
-
-## if tabular files are kept, write them to galaxy-datafile
-if ($outfiles{'loh'} ne 'None') {
-	## 
-	system("cp '$working_dir/in.dat.LOH' '".$outfiles{'loh'}."'");
-	system("cp '$working_dir/in.dat.LOH.hc' '".$outfiles{'loh'}."'");
-	system("cp '$working_dir/in.dat.Germline' '".$outfiles{'germ'}."'");
-	system("cp '$working_dir/in.dat.Germline.hc' '".$outfiles{'germ_hc'}."'");
-	system("cp '$working_dir/in.dat.Somatic' '".$outfiles{'som'}."'");
-	system("cp '$working_dir/in.dat.Somatic.hc' '".$outfiles{'som_hc'}."'");
-}
-## if vcf files are kept, generate them, and write to galaxy-datafile
-if ($outfiles{'loh_hc_vcf'} ne 'None') {
-	tab2vcf($working_dir,'in.dat.LOH.hc',$outfiles{'loh_hc_vcf'});
-	tab2vcf($working_dir,'in.dat.Germline.hc',$outfiles{'germ_hc_vcf'});
-	tab2vcf($working_dir,'in.dat.Somatic.hc',$outfiles{'som_hc_vcf'});
-}
-exit;
-
-sub tab2vcf
-{
-	my $wd = shift;
-	my $in = shift;
-	my $out = shift;
-	open OUT, ">$out";
-	print OUT "##fileformat=VCFv4.1\n";
-	print OUT "##source=processSomatic\n";
-	print OUT '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">'."\n";
-	print OUT '##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (Germline,Somatic,LOH)">'."\n";
-	print OUT '##INFO=<ID=VPV,Number=1,Type=Float,Description="Variant P-value">'."\n";
-	print OUT '##INFO=<ID=SPV,Number=1,Type=Float,Description="Somatic Variant P-value">'."\n";
-	print OUT '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">'."\n";
-	print OUT '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'."\n";
-	print OUT '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">'."\n";
-	print OUT '##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">'."\n";
-	print OUT '##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">'."\n";
-	print OUT '##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">'."\n";
-	print OUT '##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">'."\n";
-	print OUT '#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR'."\n";
-	open IN, "$wd/$in";
-	my $head = <IN>;
-	while (<IN>) {
-		chomp;
-		my @p = split(/\t/,$_);
-		my $td = $p[4] + $p[5] + $p[8] + $p[9];
-		my $vpv = sprintf('%.3E',$p[13]);
-		my $spv = sprintf('%.3E',$p[14]);
-		my $info = "DP=$td;SS=$p[12];VPV=$vpv;SPV=$spv";
-		## gt normal string
-		my $gtnormal = '';
-		if ("$p[7]" eq "$p[2]") {
-			$gtnormal = "0/0";
-		}
-		elsif ("$p[7]" eq "$p[3]") {
-			$gtnormal = "1/1";
-		}
-		else {
-			$gtnormal = "0/1";
-		}
-		my $nsum = $p[4] + $p[5];
-		$gtnormal .= ":.:$nsum:$p[4]:$p[5]:$p[6]:$p[19],$p[20],$p[21],$p[22]";
-		## gt tumor string
-		my $gttumor = '';
-		if ("$p[11]" eq "$p[2]") {
-			$gttumor = "0/0";
-		}
-		elsif ("$p[11]" eq "$p[3]") {
-			$gttumor = "1/1";
-		}
-		else {
-			$gttumor = "0/1";
-		}
-		my $tsum = $p[8] + $p[9];
-		$gttumor .= ":.:$tsum:$p[8]:$p[9]:$p[10]:$p[15],$p[16],$p[17],$p[18]";
-
-		## outline 
-		my $line = "$p[0]\t$p[1]\t.\t$p[2]\t$p[3]\t.\tPASS\t$info\tGT:GQ:DP:RD:AD:FREQ:DP4\t$gtnormal\t$gttumor\n";
-		print OUT $line;
-	}
-	close IN;
-	close OUT;
-}
-sub vs2vcf 
-{
-
-	#
-	# G l o b a l     v a r i a b l e s 
-	#
-	my $version = '0.1';
-
-	#
-	# Read in file
-	#
-	my $input = shift;
-	my $output = shift;
-	my $chr_ord = shift;
-	open(IN, $input) or die "Can't open $input': $!\n";
-	open(OUT, ">$output") or die "Can't create $output': $!\n";
-	my %output;
-
-	while ( <IN> )
-	{
-		if ( /^#/ )
-		{
-			print OUT;
-			next;
-		}
-		chomp;
-		my $line = $_;
-
-		my @flds = split ( "\t", $line );
-		my $ref = $flds[3];
-		my $alt = $flds[4];
-		#
-		# Deletion of bases
-		#
-		if ( $alt =~ /^\-/ )
-		{
-			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
-		}
-
-		#
-		# Insertion of bases
-		#
-		if ( $alt =~ /^\+/ )
-		{
-			$flds[4] = $ref.substr($alt,1);
-		}
-		## insert dot for reference positions.
-		if ($flds[4] eq '') {
-			$flds[4] = '.';
-		}
-		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
-		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
-	}
-	close(IN);
-	# if chromosome order given return in sorted order
-	if(defined $chr_ord) 
-	{
-		for my $chrom (@{ $chr_ord }) 
-		{
-			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
-			{
-				print OUT $output{$chrom}{$pos};
-			}
-		}
-	}
-	close(OUT);
-}
-
-
-sub chromosome_order 
-{
-	my $input = shift;
-	# calculate flagstats
-	my $COMM = "samtools view -H $input | grep '^\@SQ'";
-	my @SQ = `$COMM`;
-	chomp @SQ;
-	for(my $i = 0; $i <= $#SQ; $i++) 
-	{
-		$SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/;
-	} 
-	return(@SQ);
-}
-
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_processSomatic.xml
--- a/varscan_processSomatic.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,154 +0,0 @@
-<tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5">
-  <description>
-        Extract HC calls from Somatic Caller
-  </description>
-  <requirements>
-  	<requirement type="package" version="2.3.5">VarScan</requirement>
-  </requirements>
-  <command interpreter="perl">
-  	
-	varscan_processSomatic.pl 
-  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic" 
-	"INPUT::$input"
-        "LOG::$log"
-  	
-	"OPTION::--min-tumor-freq $min_tumor_freq"
-	"OPTION::--max-normal-freq $max_normal_freq"
-	"OPTION::--p-value $p_value"
-	"OUTPUT::--loh $loh"
-	"OUTPUT::--loh_hc $loh_hc"
-	"OUTPUT::--germ $germ"
-	"OUTPUT::--germ_hc $germ_hc"
-	"OUTPUT::--som $som"
-	"OUTPUT::--som_hc $som_hc"
-	"OUTPUT::--som_hc_vcf $som_hc_vcf"
-	"OUTPUT::--germ_hc_vcf $germ_hc_vcf"
-	"OUTPUT::--loh_hc_vcf $loh_hc_vcf"
-	
-  </command>
-
-  <inputs>
-
-	<param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" />
-
-	<param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/>
-	<param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/>
-	<param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/>
-	<param name="outtype" type="select" label="Output Type:" default="1">
-		<option value="0">Native VarScan Tables</option>
-		<option value="1">VCF format (only High Confidence)</option>
-		<option value="2">Both</option>
-	</param>
-
-  </inputs>
-  <outputs>
-        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " />
-        <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " >
-		<filter>outtype != "1"</filter>
-	</data>
-	<data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)">
-		<filter>outtype != "1"</filter>
-	</data>
-
-	<data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" >
-		<filter>outtype != "1"</filter>
-	</data>
-
-	<data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)">
-		<filter>outtype != "1"</filter>
-	</data>
-
-	<data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" >
-		<filter>outtype != "1"</filter>
-	</data>
-
-	<data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" >
-		<filter>outtype != "1"</filter>
-	</data>
-
-	<data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" >
-		<filter>outtype != "0"</filter>
-	</data>
-
-	<data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" >
-		<filter>outtype != "0"</filter>
-	</data>
-
-	<data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" >
-		<filter>outtype != "0"</filter>
-	</data>
-
-
-	
-
-  </outputs>
-  	
-  <help> 
-
-.. class:: infomark
-
-**What it does**
-
-::
-
- VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
-
-    Germline variants (SNPs an dindels) in individual samples or pools of samples.
-    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
-    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
-    Somatic copy number alterations (CNAs) in tumor-normal exome data.
-
-
-**Input**
-
-::
-
-  mpileup normal file - The SAMtools mpileup file for normal
-  mpileup tumor file - The SAMtools mpileup file for tumor
- 
-
-**Parameters**
-
-::
-
-  min-coverage	
-  	Minimum read depth at a position to make a call [8]
-
-  min-coverage-normal	
-  	Minimum coverage in normal to call somatic [8]
-  	
-  min-coverage-tumor	
-  	Minimum coverage in tumor to call somatic [6]
-  	
-  min-var-freq 
-  	Minimum variant frequency to call a heterozygote [0.10]  	  	
-
-  min-freq-for-hom
-  	Minimum frequency to call homozygote [0.75]
-  	
-  normal-purity 
-  	Estimated purity (non-tumor content) of normal sample [1.00]
-  	
-  tumor-purity
-  	Estimated purity (tumor content) of tumor sample [1.00]
-  
-  p-value
-  	Default p-value threshold for calling variants [0.99]
-  	
-  somatic-p-value
-  	P-value threshold to call a somatic site [0.05]  	
-  
-  strand-filter
-  	If set to 1, removes variants with >90% strand bias
-  	
-  validation 
-  	If set to 1, outputs all compared positions even if non-variant
-  
-  output-vcf
-  	If set to 1, outputs in VCF format [Default]
-
-
-  
-  </help>
-</tool>
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_somatic.native.xml
--- a/varscan_somatic.native.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-<tool id="varscan_somatic_native" name="VarScan Somatic (Native Output)" version="2.3.5">
-  <description>
-        somatic mutation caller for cancer genomics
-  </description>
-  <requirements>
-  	<requirement type="package" version="2.3.5">VarScan</requirement>
-  </requirements>
-  <command interpreter="perl">
-  	
-	varscan_somatic.pl 
-  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" 
-  	"NORMAL::$normal" 
-  	"TUMOR::$tumor"
-	"TUMORBAM::$tumorbam"
-	"SNP::$snp"
-	"INDEL::$indel"
-        "LOG::$log"
-  	
-	"OPTION::--min-coverage $min_coverage"
-	"OPTION::--min-coverage-normal $min_coverage_normal"
-	"OPTION::--min-coverage-tumor $min_coverage_tumor"
-	
-	"OPTION::--min-var-freq $min_var_freq"
-	"OPTION::--min-freq-for-hom $min_freq_for_hom"
-	
-	"OPTION::--normal-purity $normal_purity"	
-	"OPTION::--tumor-purity $tumor_purity"		
-	
-	"OPTION::--p-value $p_value"	
-	"OPTION::--somatic-p-value $somatic_p_value"	
-
-	"OPTION::--strand-filter $strand_filter"	
-	"OPTION::--validation $validation"	
-	
-
-  	
-  </command>
-
-  <inputs>
-
-	<param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
-	<param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
-	<param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
-
-	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
-	<param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
-	<param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
-	
-	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
-	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
-	
-	<param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
-	<param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
-	
-
-	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
-	<param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
-
-	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
-	<param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
-	
-  </inputs>
-  <outputs>
-        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
-	<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP)" />
-	<data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL)" />
-	
-
-  </outputs>
-  	
-  <help> 
-
-.. class:: infomark
-
-**What it does**
-
-::
-
- VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
-
-    Germline variants (SNPs an dindels) in individual samples or pools of samples.
-    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
-    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
-    Somatic copy number alterations (CNAs) in tumor-normal exome data.
-
-
-**Input**
-
-::
-
-  mpileup normal file - The SAMtools mpileup file for normal
-  mpileup tumor file - The SAMtools mpileup file for tumor
- 
-
-**Parameters**
-
-::
-
-  min-coverage	
-  	Minimum read depth at a position to make a call [8]
-
-  min-coverage-normal	
-  	Minimum coverage in normal to call somatic [8]
-  	
-  min-coverage-tumor	
-  	Minimum coverage in tumor to call somatic [6]
-  	
-  min-var-freq 
-  	Minimum variant frequency to call a heterozygote [0.10]  	  	
-
-  min-freq-for-hom
-  	Minimum frequency to call homozygote [0.75]
-  	
-  normal-purity 
-  	Estimated purity (non-tumor content) of normal sample [1.00]
-  	
-  tumor-purity
-  	Estimated purity (tumor content) of tumor sample [1.00]
-  
-  p-value
-  	Default p-value threshold for calling variants [0.99]
-  	
-  somatic-p-value
-  	P-value threshold to call a somatic site [0.05]  	
-  
-  strand-filter
-  	If set to 1, removes variants with >90% strand bias
-  	
-  validation 
-  	If set to 1, outputs all compared positions even if non-variant
-  
-  output-vcf
-  	If set to 1, outputs in VCF format [Default]
-
-
-  
-  </help>
-</tool>
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_somatic.pl
--- a/varscan_somatic.pl	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-#!/usr/bin/perl
-
-
-use strict;
-use Cwd;
-
-die qq(
-Bad numbr of inputs
-
-) if(!@ARGV);
-
-my $options ="";
-my $normal="";
-my $command="";
-my $tumor="";
-my $tumorbam = "";
-my $output="";
-my $snp="";
-my $indel="";
-my $working_dir = cwd();
-my $log = '';
-
-foreach my $input (@ARGV) 
-{
-	my @tmp = split "::", $input;
-	if($tmp[0] eq "COMMAND") 
-	{
-		$command = $tmp[1];
-	} 
-	elsif($tmp[0] eq "NORMAL") 
-	{
-		$normal = $tmp[1];
-	} 
-	elsif($tmp[0] eq "TUMOR") 
-	{
-		$tumor = $tmp[1];
-	}
-	elsif($tmp[0] eq "TUMORBAM")
-	{
-		$tumorbam = $tmp[1];
-	}
-	elsif($tmp[0] eq "OPTION") 
-	{
-		my @p = split(/\s+/,$tmp[1]);
-		if ($p[0] =~ m/validation|strand-filter|output-vcf/ && $p[1] == 0) {
-			next;
-		}
-		$options = "$options ${tmp[1]}";
-	}
-	elsif($tmp[0] eq "OUTPUT") 
-	{
-		$output = $tmp[1];
-	}
-	elsif($tmp[0] eq "SNP") 
-	{
-		$snp = $tmp[1];
-	}
-	elsif($tmp[0] eq "INDEL") 
-	{
-		$indel = $tmp[1];
-	}
-
-	elsif($tmp[0] eq "LOG")
-        {
-                $log = $tmp[1];
-        }
-	
-	else 
-	{
-		die("Unknown Input: $input\n");
-	}
-}
-
-## VCF OUTPUT 
-if ($output ne '') {
-	system ("$command $normal $tumor $options --output-snp $working_dir/out.snp --output-indel $working_dir/out.indel 2>$log");
-	my $indels = "$working_dir/out.indel.vcf";
-	my $snps = "$working_dir/out.snp.vcf";
-	
-	system("grep -v '^\#' $indels | grep -v '^chrom position' >> $snps");
-	my @chr_ord = chromosome_order($tumorbam);
-
-	vs2vcf($snps, $output,\@chr_ord);
-}
-## SNP/INDEL OUTPUT
-else {
-	system  ("$command $normal $tumor $options --output-snp $snp --output-indel $indel 2>$log");
-}
-
-sub vs2vcf 
-{
-
-	#
-	# G l o b a l     v a r i a b l e s 
-	#
-	my $version = '0.1';
-
-	#
-	# Read in file
-	#
-	my $input = shift;
-	my $output = shift;
-	my $chr_ord = shift;
-	open(IN, $input) or die "Can't open $input': $!\n";
-	open(OUT, ">$output") or die "Can't create $output': $!\n";
-	my %output;
-
-	while ( <IN> )
-	{
-		if ( /^#/ )
-		{
-			print OUT;
-			next;
-		}
-		chomp;
-		my $line = $_;
-
-		my @flds = split ( "\t", $line );
-		my $ref = $flds[3];
-		my $alt = $flds[4];
-		#
-		# Deletion of bases
-		#
-		if ( $alt =~ /^\-/ )
-		{
-			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
-		}
-
-		#
-		# Insertion of bases
-		#
-		if ( $alt =~ /^\+/ )
-		{
-			$flds[4] = $ref.substr($alt,1);
-		}
-		## insert dot for reference positions.
-		if ($flds[4] eq '') {
-			$flds[4] = '.';
-		}
-		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
-		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
-	}
-	close(IN);
-	# if chromosome order given return in sorted order
-	if(defined $chr_ord) 
-	{
-		for my $chrom (@{ $chr_ord }) 
-		{
-			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
-			{
-				print OUT $output{$chrom}{$pos};
-			}
-		}
-	}
-	close(OUT);
-}
-
-
-sub chromosome_order 
-{
-	my $input = shift;
-	# calculate flagstats
-	my $COMM = "samtools view -H $input | grep '^\@SQ'";
-	my @SQ = `$COMM`;
-	chomp @SQ;
-	for(my $i = 0; $i <= $#SQ; $i++) 
-	{
-		$SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/;
-	} 
-	return(@SQ);
-}
-
-
diff -r b2ad469e0ff9 -r 572397bbe057 varscan_somatic.xml
--- a/varscan_somatic.xml	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-<tool id="varscan_somatic_vcf" name="VarScan Somatic (VCF Output)" version="2.3.5">
-  <description>
-        somatic mutation caller for cancer genomics
-  </description>
-  <requirements>
-  	<requirement type="package" version="2.3.5">VarScan</requirement>
-  </requirements>
-  <command interpreter="perl">
-  	
-	varscan_somatic.pl 
-  	"COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" 
-  	"NORMAL::$normal" 
-  	"TUMOR::$tumor"
-	"TUMORBAM::$tumorbam"
-  	"OUTPUT::$output"
-        "LOG::$log"
-  	
-	"OPTION::--min-coverage $min_coverage"
-	"OPTION::--min-coverage-normal $min_coverage_normal"
-	"OPTION::--min-coverage-tumor $min_coverage_tumor"
-	
-	"OPTION::--min-var-freq $min_var_freq"
-	"OPTION::--min-freq-for-hom $min_freq_for_hom"
-	
-	"OPTION::--normal-purity $normal_purity"	
-	"OPTION::--tumor-purity $tumor_purity"		
-	
-	"OPTION::--p-value $p_value"	
-	"OPTION::--somatic-p-value $somatic_p_value"	
-
-	"OPTION::--strand-filter $strand_filter"	
-	"OPTION::--validation $validation"	
-	"OPTION::--output-vcf 1"	
-	
-
-  	
-  </command>
-
-  <inputs>
-
-	<param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
-	<param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
-	<param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
-
-	<param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
-	<param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
-	<param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
-	
-	<param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
-	<param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
-	
-	<param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
-	<param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
-	
-
-	<param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
-	<param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
-
-	<param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
-	<param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
-	
-  </inputs>
-  <outputs>
-  	<data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
-        <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
-	<!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
-	<data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
-	
-
-  </outputs>
-  	
-  <help> 
-
-.. class:: infomark
-
-**What it does**
-
-::
-
- VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:
-
-    Germline variants (SNPs an dindels) in individual samples or pools of samples.
-    Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
-    Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
-    Somatic copy number alterations (CNAs) in tumor-normal exome data.
-
-
-**Input**
-
-::
-
-  mpileup normal file - The SAMtools mpileup file for normal
-  mpileup tumor file - The SAMtools mpileup file for tumor
- 
-
-**Parameters**
-
-::
-
-  min-coverage	
-  	Minimum read depth at a position to make a call [8]
-
-  min-coverage-normal	
-  	Minimum coverage in normal to call somatic [8]
-  	
-  min-coverage-tumor	
-  	Minimum coverage in tumor to call somatic [6]
-  	
-  min-var-freq 
-  	Minimum variant frequency to call a heterozygote [0.10]  	  	
-
-  min-freq-for-hom
-  	Minimum frequency to call homozygote [0.75]
-  	
-  normal-purity 
-  	Estimated purity (non-tumor content) of normal sample [1.00]
-  	
-  tumor-purity
-  	Estimated purity (tumor content) of tumor sample [1.00]
-  
-  p-value
-  	Default p-value threshold for calling variants [0.99]
-  	
-  somatic-p-value
-  	P-value threshold to call a somatic site [0.05]  	
-  
-  strand-filter
-  	If set to 1, removes variants with >90% strand bias
-  	
-  validation 
-  	If set to 1, outputs all compared positions even if non-variant
-  
-  output-vcf
-  	If set to 1, outputs in VCF format [Default]
-
-
-  
-  </help>
-</tool>
-