Output AO using bcftools

Question

[L. A. Liggett]

I calling variants from sorted bam files using samtools mpileup and then bcftools call -cv input > output.vcf. But in the resulting variant file there is no data reported for alternate allele frequency or AO. Is there a way to get bcftools to output AO?

Answer 1

[Jorge Amigo]

you're looking for

bcftools plugin fill-AN-AC

although the plugins' installation is not documented in the manual. you'll have to make sure that you compile the plugins along with the bcftools executable, and set the environment variable BCFTOOLS_PLUGINS appropriately.