calculating genotype quality from genotype likelihood
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5.6 years ago
Ana ▴ 200

Hi all, I have faced with a question and I would appreciate if anyone has any comment or suggestion. I have got a vcf file made by FreeBayes, genotype quality is missing. I want to filter out those below the cutoff value. Therefore I want to know how can I get (calculate) genotype quality from genotype likelihood? This is my genotype field:

GT:DP:DPR:RO:QR:AO:QA:GL    ./0:11:4,0:7:255:0:0:-7.21754,-9.32475,-22.6408

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FreeBayes genotype likelihood genotype quality • 2.5k views
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5.6 years ago
youcai ▴ 60

bcftools may be help

bcftools view

Consensus/variant calling options:

       -c        SNP calling (force -e)
       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]
       -e        likelihood based analyses
       -g        call genotypes at variant sites (force -c)
       -i FLOAT  indel-to-substitution ratio [-1]
       -I        skip indels
       -m FLOAT  alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT
       -p FLOAT  variant if P(ref|D)<FLOAT [0.5]
       -P STR    type of prior: full, cond2, flat [full]
       -t FLOAT  scaled substitution mutation rate [0.001]
       -T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]
       -v        output potential variant sites only (force -c)
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I actually did find some ideas from the post by Philip How to interpret genotype likelihoods? They suggested to calculate genotype likelihood ratio. Does any one have any idea about good threshold value for this?

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