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view test-data/norm.vcf @ 11:8bb5efd7a3dd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
author iuc
date Wed, 25 Dec 2019 12:25:07 -0500
parents b068ef999550
children
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
##contig=<ID=1,length=2147483647>
##contig=<ID=2,length=2147483647>
##contig=<ID=3,length=2147483647>
##contig=<ID=4,length=2147483647>
##contig=<ID=5,length=2147483647>
##contig=<ID=20,length=2147483647>
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
1	105	.	TAAACCCTAAA	TAA,TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF
2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
20	5	.	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
20	80	.	CACAG	CACAT	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
20	95	.	TCACCG	ACACCG	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
20	95	.	TCACCG	AAAAAA	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
20	273	.	CAAAAAAAAAAAAAAAAAAAAA	CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=4;AC=2,2	GT:PL:DP	1/2:0,3,5,3,5,5:1	1/2:0,3,5,3,5,5:1
20	274	.	AAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
20	275	.	A	C,G	999	PASS	INDEL;AN=2;AC=0,2	GT:PL:DP:FGF:FGI:FGS:FSTR	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
3	15	.	CACA	CAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
4	21	.	ATTTTTTTTTTTTTTTC	ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
5	22	.	A	AGA	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0