Mercurial > repos > takadonet > bcftools_view
comparison test-data/view.3.out @ 0:667b2d503ba3 draft default tip
Uploaded
| author | takadonet |
|---|---|
| date | Wed, 08 Apr 2015 12:09:16 -0400 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:667b2d503ba3 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##FILTER=<ID=PASS,Description="All filters passed"> | |
| 3 ##reference=file:///seq/references/1000Genomes-NCBI37.fasta | |
| 4 ##contig=<ID=11,length=135006516> | |
| 5 ##contig=<ID=20,length=63025520> | |
| 6 ##contig=<ID=X,length=155270560> | |
| 7 ##contig=<ID=Y,length=59373566> | |
| 8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> | |
| 9 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> | |
| 10 ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions"> | |
| 11 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | |
| 12 ##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction"> | |
| 13 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)"> | |
| 14 ##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F"> | |
| 15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | |
| 16 ##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> | |
| 17 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> | |
| 18 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads"> | |
| 19 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> | |
| 20 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth"> | |
| 21 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> | |
| 22 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| 23 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> | |
| 24 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 25 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> | |
| 27 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]"> | |
| 28 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]"> | |
| 29 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]"> | |
| 30 ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]"> | |
| 31 ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]"> | |
| 32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 | |
| 33 X 2928329 rs62584840 C T 999 PASS DP4=302,9137,32,1329;DP=11020;Dels=0;FS=13.38;HWE=0.284332;ICF=0.0253;MQ0=0;MQ=49;PV4=0.094,0,0,1;QD=18.61;AN=2;AC=1 GT:PL:DP:GQ 0/1:73,0,19:4:30 | |
| 34 X 2933066 rs61746890 G C 999 PASS DP4=69865,100561,461,783;DP=173729;Dels=0;FS=10.833;MQ0=0;MQ=50;PV4=0.005,3.6e-14,0,1;QD=15.33;AN=2;AC=1 GT:PL:DP:GQ 0/1:255,255,255:62:99 |