Mercurial > repos > iuc > bcftools_plugin_missing2ref
diff test-data/norm.merge.vcf @ 0:5e9cf5308e97 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
| author | iuc |
|---|---|
| date | Wed, 06 Jul 2016 07:07:16 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm.merge.vcf Wed Jul 06 07:07:16 2016 -0400 @@ -0,0 +1,61 @@ +##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=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"> +##FILTER=<ID=FAIL1,Description="Failed filter 1"> +##FILTER=<ID=FAIL2,Description="Failed filter 2"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002 +1 105 . TAAACCCTAAA TAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC +1 105 . TAAACCCTAAA TAACCCTAAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,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 999 FAIL1 INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1 +2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1 +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 . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1 +20 5 id0001 TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 +20 5 id0002 TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1 +20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1 +20 59 id0003 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 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:0,3,5:1 1/0:0,3,5:1 +20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:0,3,5:1 0/1:0,3,5:1 +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 0 FAIL1 INDEL;AN=2;AC=0 GT:PL:DP:FGF:FGI:FGS:FSTR 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD +20 275 . A G 0 FAIL2 INDEL;AN=2;AC=2 GT:PL:DP:FGF:FGI:FGS:FSTR 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD +20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 +20 300 . A C 998 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 +20 300 . A G 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0