diff test-data/cnv_baf_only.vcf @ 8:9b298d4d10c2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:16:01 -0400
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cnv_baf_only.vcf	Wed Jun 05 13:16:01 2019 -0400
@@ -0,0 +1,188 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test
+10	135656	rs10904561	T	G	.	.	.	GT:BAF	0/1:0.5176
+10	135708	rs7917054	G	A	.	.	.	GT:BAF	1/0:0.501
+10	178434	rs7089889	T	G	.	.	.	GT:BAF	0/1:0.4833
+10	188805	rs12146291	A	G	.	.	.	GT:BAF	0/1:0.4715
+10	203471	rs10903451	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	252693	rs2379078	T	C	.	.	.	GT:BAF	0/0:0.0068
+10	273344	rs2448378	A	C	.	.	.	GT:BAF	0/0:0.0000
+10	279248	rs2496278	C	A	.	.	.	GT:BAF	1/0:0.6268
+10	291134	rs10508201	T	C	.	.	.	GT:BAF	0/1:0.4723
+10	293358	exm2249181	A	C	.	.	.	GT:BAF	0/0:0.0044
+10	313504	rs4880568	C	T	.	.	.	GT:BAF	1/1:0.9803
+10	317501	rs2018975	C	T	.	.	.	GT:BAF	0/0:0
+10	323283	rs3740304	A	G	.	.	.	GT:BAF	0/1:0.5588
+10	326894	rs3125027	T	C	.	.	.	GT:BAF	0/0:0.0005
+10	327162	exm805022	C	T	.	.	.	GT:BAF	0/0:0
+10	329493	rs3815985	C	A	.	.	.	GT:BAF	1/0:0.5187
+10	338553	rs3125031	C	T	.	.	.	GT:BAF	1/0:0.4696
+10	354301	rs35198327	C	T	.	.	.	GT:BAF	1/0:0.4929
+10	375475	variant.11341	C	T	.	.	.	GT:BAF	0/0:0.000199999999999978
+10	377161	rs7070654	C	T	.	.	.	GT:BAF	0/0:0
+10	387060	rs7904155	G	A	.	.	.	GT:BAF	1/1:0.9945
+10	390962	exm805090	G	A	.	.	.	GT:BAF	0/0:9.9999999999989e-05
+10	390983	exm805091	G	A	.	.	.	GT:BAF	0/0:0
+10	394615	exm805105	G	A	.	.	.	GT:BAF	0/0:0
+10	402390	exm805131	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	403792	exm805136	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	410501	exm805166	C	T	.	.	.	GT:BAF	0/0:0
+10	413010	rs9787422	C	T	.	.	.	GT:BAF	1/0:0.5334
+10	423555	rs12245012	G	A	.	.	.	GT:BAF	0/0:0.00149999999999995
+10	423671	rs10904067	C	T	.	.	.	GT:BAF	1/0:0.5566
+10	431161	exm2271240	C	T	.	.	.	GT:BAF	1/0:0.4838
+10	435971	exm2249233	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	435990	exm805214	G	A	.	.	.	GT:BAF	0/0:0
+10	453567	rs4881254	C	T	.	.	.	GT:BAF	1/0:0.5079
+10	462885	rs10904173	G	A	.	.	.	GT:BAF	1/0:0.4819
+10	465046	exm805254	G	A	.	.	.	GT:BAF	0/0:0
+10	468599	rs12415961	T	C	.	.	.	GT:BAF	0/1:0.5021
+10	486935	exm805280	G	C	.	.	.	GT:BAF	0/0:0.0186
+10	487973	rs4881313	T	C	.	.	.	GT:BAF	0/1:0.5628
+10	521431	exm2271370	C	T	.	.	.	GT:BAF	1/1:0.9952
+10	521723	rs4881336	C	T	.	.	.	GT:BAF	1/1:1
+10	547567	rs816599	A	G	.	.	.	GT:BAF	1/1:1.0000
+10	554186	rs12251997	C	T	.	.	.	GT:BAF	0/0:0.00309999999999999
+10	556129	rs10466270	A	G	.	.	.	GT:BAF	0/1:0.5142
+10	566379	rs11252926	C	T	.	.	.	GT:BAF	1/0:0.5024
+10	588406	rs10904450	A	G	.	.	.	GT:BAF	0/0:0.0006
+10	592283	rs816646	G	A	.	.	.	GT:BAF	1/0:0.5006
+10	601089	rs816650	C	T	.	.	.	GT:BAF	0/0:0
+10	615782	rs17221309	G	A	.	.	.	GT:BAF	0/0:0.00319999999999998
+10	635857	rs7069611	T	C	.	.	.	GT:BAF	0/0:0.0013
+10	669358	rs7898821	G	A	.	.	.	GT:BAF	0/0:0
+10	673037	rs816563	C	T	.	.	.	GT:BAF	1/1:0.9065
+10	680428	rs2124585	G	A	.	.	.	GT:BAF	1/0:0.5212
+10	712617	rs17136372	A	C	.	.	.	GT:BAF	1/1:0.9992
+10	738630	rs1750792	C	T	.	.	.	GT:BAF	0/0:0
+10	749238	rs553326	G	T	.	.	.	GT:BAF	0/0:0.00229999999999997
+10	754033	rs2265090	C	A	.	.	.	GT:BAF	0/0:0
+10	757222	rs10904546	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	766105	rs7906313	T	C	.	.	.	GT:BAF	0/0:0.0116
+10	776027	rs11253377	C	T	.	.	.	GT:BAF	1/1:0.9964
+10	787896	rs1769242	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	800213	rs2254501	G	A	.	.	.	GT:BAF	1/1:0.9918
+10	802445	rs1769215	C	T	.	.	.	GT:BAF	0/0:0.00370000000000004
+10	803721	rs2790381	C	T	.	.	.	GT:BAF	1/1:0.9798
+10	811876	rs12414585	G	A	.	.	.	GT:BAF	1/0:0.516
+10	813426	rs11253424	C	T	.	.	.	GT:BAF	0/0:0
+10	815149	rs7084027	A	G	.	.	.	GT:BAF	1/1:0.9944
+10	820868	rs10752019	C	T	.	.	.	GT:BAF	0/0:0.0118
+10	833528	exm2271241	T	G	.	.	.	GT:BAF	0/1:0.4896
+10	834736	rs4881530	G	A	.	.	.	GT:BAF	0/0:0.00249999999999995
+10	836115	rs11253444	A	G	.	.	.	GT:BAF	0/1:0.5199
+10	838179	rs1536337	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	858022	rs9124	C	T	.	.	.	GT:BAF	0/0:0
+10	858924	exm805329	G	A	.	.	.	GT:BAF	0/0:0
+10	859047	exm805338	C	A	.	.	.	GT:BAF	0/0:0
+10	860687	exm805350	C	T	.	.	.	GT:BAF	0/0:0
+10	860726	exm805354	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	860970	exm805360	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	871110	exm805378	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	871746	exm805386	G	A	.	.	.	GT:BAF	0/0:0.00239999999999996
+10	875350	exm805392	G	A	.	.	.	GT:BAF	0/0:0
+10	888899	exm805400	C	T	.	.	.	GT:BAF	0/0:0.00470000000000004
+10	888916	exm805401	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	894838	rs12249828	C	T	.	.	.	GT:BAF	1/0:0.4839
+10	903950	rs11253471	A	G	.	.	.	GT:BAF	0/1:0.4747
+10	909757	exm805413	G	A	.	.	.	GT:BAF	0/0:0
+10	909766	exm805415	G	A	.	.	.	GT:BAF	0/0:0
+10	910074	exm805420	C	T	.	.	.	GT:BAF	0/0:0.0071
+10	910081	exm805421	C	T	.	.	.	GT:BAF	0/0:0.002
+10	927331	rs11253489	G	A	.	.	.	GT:BAF	1/0:0.5325
+10	931618	exm805430	G	A	.	.	.	GT:BAF	0/0:0
+10	931631	exm805431	C	T	.	.	.	GT:BAF	0/0:0.00390000000000001
+11	135656	rs10904561	T	G	.	.	.	GT:BAF	0/1:0.5176
+11	135708	rs7917054	G	A	.	.	.	GT:BAF	1/0:0.501
+11	178434	rs7089889	T	G	.	.	.	GT:BAF	0/1:0.4833
+11	188805	rs12146291	A	G	.	.	.	GT:BAF	0/1:0.4715
+11	203471	rs10903451	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	252693	rs2379078	T	C	.	.	.	GT:BAF	0/0:0.0068
+11	273344	rs2448378	A	C	.	.	.	GT:BAF	0/0:0.0000
+11	279248	rs2496278	C	A	.	.	.	GT:BAF	1/0:0.6268
+11	291134	rs10508201	T	C	.	.	.	GT:BAF	0/1:0.4723
+11	293358	exm2249181	A	C	.	.	.	GT:BAF	0/0:0.0044
+11	313504	rs4880568	C	T	.	.	.	GT:BAF	1/1:0.9803
+11	317501	rs2018975	C	T	.	.	.	GT:BAF	0/0:0
+11	323283	rs3740304	A	G	.	.	.	GT:BAF	0/1:0.5588
+11	326894	rs3125027	T	C	.	.	.	GT:BAF	0/0:0.0005
+11	327162	exm805022	C	T	.	.	.	GT:BAF	0/0:0
+11	329493	rs3815985	C	A	.	.	.	GT:BAF	1/0:0.5187
+11	338553	rs3125031	C	T	.	.	.	GT:BAF	1/0:0.4696
+11	354301	rs35198327	C	T	.	.	.	GT:BAF	1/0:0.4929
+11	375475	variant.11341	C	T	.	.	.	GT:BAF	0/0:0.000199999999999978
+11	377161	rs7070654	C	T	.	.	.	GT:BAF	0/0:0
+11	387060	rs7904155	G	A	.	.	.	GT:BAF	1/1:0.9945
+11	390962	exm805090	G	A	.	.	.	GT:BAF	0/0:9.9999999999989e-05
+11	390983	exm805091	G	A	.	.	.	GT:BAF	0/0:0
+11	394615	exm805105	G	A	.	.	.	GT:BAF	0/0:0
+11	402390	exm805131	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	403792	exm805136	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	410501	exm805166	C	T	.	.	.	GT:BAF	0/0:0
+11	413010	rs9787422	C	T	.	.	.	GT:BAF	1/0:0.5334
+11	423555	rs12245012	G	A	.	.	.	GT:BAF	0/0:0.00149999999999995
+11	423671	rs10904067	C	T	.	.	.	GT:BAF	1/0:0.5566
+11	431161	exm2271240	C	T	.	.	.	GT:BAF	1/0:0.4838
+11	435971	exm2249233	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	435990	exm805214	G	A	.	.	.	GT:BAF	0/0:0
+11	453567	rs4881254	C	T	.	.	.	GT:BAF	1/0:0.5079
+11	462885	rs10904173	G	A	.	.	.	GT:BAF	1/0:0.4819
+11	465046	exm805254	G	A	.	.	.	GT:BAF	0/0:0
+11	468599	rs12415961	T	C	.	.	.	GT:BAF	0/1:0.5021
+11	486935	exm805280	G	C	.	.	.	GT:BAF	0/0:0.0186
+11	487973	rs4881313	T	C	.	.	.	GT:BAF	0/1:0.5628
+11	521431	exm2271370	C	T	.	.	.	GT:BAF	1/1:0.9952
+11	521723	rs4881336	C	T	.	.	.	GT:BAF	1/1:1
+11	547567	rs816599	A	G	.	.	.	GT:BAF	1/1:1.0000
+11	554186	rs12251997	C	T	.	.	.	GT:BAF	0/0:0.00309999999999999
+11	556129	rs10466270	A	G	.	.	.	GT:BAF	0/1:0.5142
+11	566379	rs11252926	C	T	.	.	.	GT:BAF	1/0:0.5024
+11	588406	rs10904450	A	G	.	.	.	GT:BAF	0/0:0.0006
+11	592283	rs816646	G	A	.	.	.	GT:BAF	1/0:0.5006
+11	601089	rs816650	C	T	.	.	.	GT:BAF	0/0:0
+11	615782	rs17221309	G	A	.	.	.	GT:BAF	0/0:0.00319999999999998
+11	635857	rs7069611	T	C	.	.	.	GT:BAF	0/0:0.0013
+11	669358	rs7898821	G	A	.	.	.	GT:BAF	0/0:0
+11	673037	rs816563	C	T	.	.	.	GT:BAF	1/1:0.9065
+11	680428	rs2124585	G	A	.	.	.	GT:BAF	1/0:0.5212
+11	712617	rs17136372	A	C	.	.	.	GT:BAF	1/1:0.9992
+11	738630	rs1750792	C	T	.	.	.	GT:BAF	0/0:0
+11	749238	rs553326	G	T	.	.	.	GT:BAF	0/0:0.00229999999999997
+11	754033	rs2265090	C	A	.	.	.	GT:BAF	0/0:0
+11	757222	rs10904546	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	766105	rs7906313	T	C	.	.	.	GT:BAF	0/0:0.0116
+11	776027	rs11253377	C	T	.	.	.	GT:BAF	1/1:0.9964
+11	787896	rs1769242	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	800213	rs2254501	G	A	.	.	.	GT:BAF	1/1:0.9918
+11	802445	rs1769215	C	T	.	.	.	GT:BAF	0/0:0.00370000000000004
+11	803721	rs2790381	C	T	.	.	.	GT:BAF	1/1:0.9798
+11	811876	rs12414585	G	A	.	.	.	GT:BAF	1/0:0.516
+11	813426	rs11253424	C	T	.	.	.	GT:BAF	0/0:0
+11	815149	rs7084027	A	G	.	.	.	GT:BAF	1/1:0.9944
+11	820868	rs10752019	C	T	.	.	.	GT:BAF	0/0:0.0118
+11	833528	exm2271241	T	G	.	.	.	GT:BAF	0/1:0.4896
+11	834736	rs4881530	G	A	.	.	.	GT:BAF	0/0:0.00249999999999995
+11	836115	rs11253444	A	G	.	.	.	GT:BAF	0/1:0.5199
+11	838179	rs1536337	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	858022	rs9124	C	T	.	.	.	GT:BAF	0/0:0
+11	858924	exm805329	G	A	.	.	.	GT:BAF	0/0:0
+11	859047	exm805338	C	A	.	.	.	GT:BAF	0/0:0
+11	860687	exm805350	C	T	.	.	.	GT:BAF	0/0:0
+11	860726	exm805354	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	860970	exm805360	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	871110	exm805378	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	871746	exm805386	G	A	.	.	.	GT:BAF	0/0:0.00239999999999996
+11	875350	exm805392	G	A	.	.	.	GT:BAF	0/0:0
+11	888899	exm805400	C	T	.	.	.	GT:BAF	0/0:0.00470000000000004
+11	888916	exm805401	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	894838	rs12249828	C	T	.	.	.	GT:BAF	1/0:0.4839
+11	903950	rs11253471	A	G	.	.	.	GT:BAF	0/1:0.4747
+11	909757	exm805413	G	A	.	.	.	GT:BAF	0/0:0
+11	909766	exm805415	G	A	.	.	.	GT:BAF	0/0:0
+11	910074	exm805420	C	T	.	.	.	GT:BAF	0/0:0.0071
+11	910081	exm805421	C	T	.	.	.	GT:BAF	0/0:0.002
+11	927331	rs11253489	G	A	.	.	.	GT:BAF	1/0:0.5325
+11	931618	exm805430	G	A	.	.	.	GT:BAF	0/0:0
+11	931631	exm805431	C	T	.	.	.	GT:BAF	0/0:0.00390000000000001