3,045
edits
Changes
From Genome Analysis Wiki
→Records
You can obtain the same output by using the following command
${GC}/bin/vt view -i 22:3699087836662041-36990879 36662041 ${OUT}/indel/final/all.genotypes.vcf.gz
* -i specifies the region
* You can leave it out and look at all the records
AF=0.017 : allele frequency based on AC/AN
GC=55,2,0 : genotype counts for 0/0, 0/1, 1/1
GF=0.5596,0.3404,0.10 : genotype frequencies based on GC
NS=57 : no. of samples
HWEAF=0.28 020 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium HWEGF=0.5296,0.4004,0.08 00 : genotype frequency derived from HWEAF HWE_LPVAL=-10.08 18 : log p value of HWE test FIC=-0.07 003 : genotype likelihood based inbreeding coefficient AB=0.61 38 : genotype likelihood based allele balance
=====GENOTYPE field=====
0/0 : homozygous reference chosen based on PL
0,96,158 145 : PHRED scaled genotype likelihoods
3 : no. of reads covering this variant
counts of reads supporting the reference allele,
the alternative allele and neither alleles respectively.
coverage of the read over the locus
or simply an allele that is not accounted for.
== INDEL Analysis ==
