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Revision as of 01:07, 6 December 2014
, 01:07, 6 December 2014→Header
==== Header ====
==== Header ====
First, let's look at the header:
First, let's look at the header:
${GC}/bin/tabix -H ${OUT}/final/all.genotypes.vcf.gz
${GC}/bin/tabix -H ${OUT}/indel/final/all.genotypes.vcf.gz
The header is as follows:
The header is as follows:
<pre>
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=22,length=51304566>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
##FORMAT=<ID=AD,Number=3,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate Allele Counts">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Number Allele Counts">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate Allele Frequency">
##INFO=<ID=GC,Number=G,Type=Integer,Description="Genotype Counts">
##INFO=<ID=GN,Number=1,Type=Integer,Description="Total Number of Genotypes Counts">
##INFO=<ID=GF,Number=G,Type=Float,Description="Genotype Frequency">
##INFO=<ID=HWEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency assuming HWE">
##INFO=<ID=HWEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency assuming HWE">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency">
##INFO=<ID=MLEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency">
##INFO=<ID=HWE_LLR,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg ln(Likelihood Ratio)">
##INFO=<ID=HWE_LPVAL,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic ln(p-value)">
##INFO=<ID=HWE_DF,Number=1,Type=Integer,Description="Degrees of freedom for Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic">
##INFO=<ID=FIC,Number=1,Type=Float,Description="Genotype likelihood based Inbreeding Coefficient">
##INFO=<ID=AB,Number=1,Type=Float,Description="Genotype likelihood based Allele Balance">
##FILTER=<ID=overlap,Description="Overlapping variant">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00641 HG00640 HG00551 HG00553 HG00554 HG00637 HG00638 HG00734 HG00736 HG00737 HG00739 HG00740 HG01047 HG01049 HG01051 HG01052 HG01054 HG01055 HG01060 HG01061 HG01066 HG01067 HG01069 HG01070 HG01072 HG01073 HG01075 HG01079 HG01080 HG01082 HG01083 HG01094 HG01097 HG01098 HG01101 HG01102 HG01107 HG01108 HG01110 HG01111 HG01167 HG01168 HG01170 HG01171 HG01173 HG01174 HG01176 HG01177 HG01182 HG01183 HG01187 HG01188 HG01190 HG01191 HG01197 HG01198 HG01204 HG01205 HG01241 HG01242 HG01247 HG01248
</pre>
Using [[Vt]], we can see the same output
Using [[Vt]], we can see the same output
${GC}/bin/vt view -H ${OUT}/final/all.genotypes.vcf.gz
${GC}/bin/vt view -H ${OUT}/indel/final/all.genotypes.vcf.gz
====Records====
====Records====
