vcf SNP file minor allele frequency filter?
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Entering edit mode
9.0 years ago
sun.nation ▴ 140

I want to filter vcf file with minor allele frequency of 30% = 0.3. I tried with: --maf 0.3

vcftools \
  --vcf ps-pt.bcf.vcf \
  --out ps-pt.bcf.vcf-5dp-miss0 \
  --remove-filtered-all \
  --maf .3 \
  --max-missing-count 0 \
  --minDP 5 \
  --minQ 10 \
  --minGQ 10 \
  --recode \
  --recode-INFO-all

But, when I checked the alignment and some het positions. Het was called such as G/T (1 read with G and 9 reads with T). I want like this (3 out of 10 reads should be G to be called GT in minimum)

I want to filter per individual not by combining all.Thanks for your suggestions.

vcf minor-allele SNP vcftools • 5.9k views
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Entering edit mode

I think you are confusing minor allele frequency (the frequency of the rare allele observed among different samples) with allele balance (the ratio of reads showing the reference sequence versus the reads showing the alt sequence, at a given site, in one individual).

I am unsure if vcftools has a filter option for allele balance. I know GATK does: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_AlleleBalanceBySample.php

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