Mercurial > repos > jjohnson > bcftools_convert_from_vcf
diff test-data/norm.setref.vcf @ 0:d396503fdbdb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
| author | jjohnson |
|---|---|
| date | Sat, 25 Jun 2016 20:47:20 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm.setref.vcf Sat Jun 25 20:47:20 2016 -0400 @@ -0,0 +1,45 @@ +##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"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002 +1 105 . TAACCCTAAA TAAACCCTAAA,TAA 999 PASS INDEL;AN=4;AC=2,2;DP=19 GT 1/2 1/2 +2 101 . . c 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 +2 105 . n <DEL> 999 PASS END=112;AN=4;AC=3 GT:DP 0/1:1 1/1:1 +2 115 . t c 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 +20 3 . c g 999 PASS INDEL;AN=4;AC=1 GT 0/0 0/1 +20 3 . gact gatg 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 +20 10 . . . 999 PASS INDEL;AN=4;AC=1 GT 1/0 0/0 +20 275 . g c,a,t,aaa 999 PASS INDEL;AN=2;AC=0,2,0,0 GT 2 2