Mercurial > repos > takadonet > bcftools_view
diff test-data/view.1.out @ 0:667b2d503ba3 draft default tip
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| author | takadonet |
|---|---|
| date | Wed, 08 Apr 2015 12:09:16 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/view.1.out Wed Apr 08 12:09:16 2015 -0400 @@ -0,0 +1,39 @@ +##fileformat=VCFv4.1 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=file:///seq/references/1000Genomes-NCBI37.fasta +##contig=<ID=11,length=135006516> +##contig=<ID=20,length=63025520> +##contig=<ID=X,length=155270560> +##contig=<ID=Y,length=59373566> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions"> +##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)"> +##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by 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"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]"> +##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]"> +##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]"> +##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]"> +##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00002 +20 138125 rs2298108 G T 999 PASS DP4=174391,20849,82080,4950;DP=286107;Dels=0;FS=3200;HWE=0.199462;ICF=0.01858;MQ0=0;MQ=46;PV4=0,0,0,1;QD=17.22;AN=2;AC=1 GT:PL:DP:GQ 0/1:140,0,255:71:99 +20 138148 rs2298109 C T 999 PASS DP4=194136,45753,94945,14367;DP=356657;Dels=0;FS=3200;HWE=0.177865;ICF=0.0198;MQ0=0;MQ=47;PV4=0,0,0,1;QD=14.57;AN=2;AC=1 GT:PL:DP:GQ 0/1:192,0,255:82:99 +20 304568 . C T 999 PASS DP4=16413,4543,945,156;DP=43557;Dels=0;FS=3200;HWE=0.076855;ICF=0.0213;MQ0=0;MQ=50;PV4=0,0,0,1;QD=15.45;AN=2;AC=1 GT:PL:DP:GQ 0|1:192,0,255:13:99 +X 2942109 rs5939407 T C 999 PASS DP4=23273,27816,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=1;AC=1 GT:PL:DP:GQ 1:255,0:33:99 +X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=1;AC=1 GT:PL:DP:GQ 1:255,0:33:99 +Y 8657215 . C A 999 PASS DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=1;AC=1 GT:PL:DP:GQ 1:255,0:64:99 +Y 10011673 rs78249411 G A 999 MinAB DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=1;AC=1 GT:PL:DP:GQ 1:95,0:130:99