Question: Calculating genotype likelihood from vcf file which has allele frequency, total no. of allele in called genotype, total no. of alternate allele
gravatar for ricchasethi
6.2 years ago by
ricchasethi0 wrote:

I am new to understanding vcf file format and have recently downloaded phase3 released data from 1000 genome project. The vcf file downloaded gives the genotype, allele frequency, total no, of alternate alleles and total no. of population considered. But it doesn't mention genotype likelihood. I'm struggling to figure out how that can be interpreted from it. Can anyone help me figure out that?


snp next-gen forum • 3.0k views
ADD COMMENTlink modified 6.1 years ago by Adam1.0k • written 6.2 years ago by ricchasethi0

Without fastq quality information you cannot calculate genotype likelihoods.  I believe you are looking at the "prerelease" data.  The full release will have genotype likelihoods.  I'm pretty sure the full phase 3 release is already out.


ADD REPLYlink written 6.1 years ago by Zev.Kronenberg11k
gravatar for Vivek
6.1 years ago by
Vivek2.4k wrote:

You cannot calculate genotype likelihood on a population. You'd need to look at individual sample level VCFs for that information.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Vivek2.4k
gravatar for Adam
6.1 years ago by
United States
Adam1.0k wrote:

I believe the files you're looking for are on the 1000 Genomes FTP in the following folder: /vol1/ftp/release/20130502/supporting/genotype_likelihoods

ADD COMMENTlink written 6.1 years ago by Adam1.0k
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