Calculating genotype likelihood from vcf file which has allele frequency, total no. of allele in called genotype, total no. of alternate allele
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6.8 years ago

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?

Thanks

SNP Forum next-gen • 3.2k views
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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.

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6.7 years ago
Vivek ★ 2.5k

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

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6.7 years ago
Adam ★ 1.0k

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

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