Question: SNP filtering by allele fraction
gravatar for drowl1
27 days ago by
drowl130 wrote:


I have a multi-sample VCF generated by GATK with an additional 'Allele fraction' (AF) annotation in the FORMAT field.

I wish to filter the SNPs in the VCF at the sample genotype-level using the AF in the FORMAT field and I want to remove sites with missing values (".") but without removing the whole variant.

I have tried the command GATK SelectVariant --select 'vc.hasAttribute("AF")' but that doesn't work.

Does anyone know of a simple way or a tool that could accomplish this?

Suggestions highly appreciated!

sequencing snp genome • 113 views
ADD COMMENTlink written 27 days ago by drowl130

Hi Could you please post an example of your table and the output you want to obtain after filtering.

ADD REPLYlink written 27 days ago by hugo.avila40


I figured it out eventually. So the reason why I thought to remove sites with missing values was because when I tried a 0.5 filter threshold with the command - bcftools view -e 'FORMAT/AF[*] => 0.5', the whole variant was excluded for all samples even if only one of the sites failed the threshold or had missing values.

The command bcftools view -i 'MIN(FMT/AF)>=0.5' worked well by keeping the whole variant and just excluding sites that failed the threshold.


ADD REPLYlink written 26 days ago by drowl130
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