Mercurial > repos > iuc > bcftools_plugin_missing2ref
view test-data/norm.vcf @ 7:31c096c6b156 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
| author | iuc |
|---|---|
| date | Thu, 21 Feb 2019 16:02:30 -0500 |
| parents | 5e9cf5308e97 |
| 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