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Question: Output AO using bcftools
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gravatar for L. A. Liggett
3.7 years ago by
L. A. Liggett • 120
Broad Institute, Harvard Medical School, Boston Children's
L. A. Liggett • 120 wrote:

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?
sequencing alignment • 1.1k views
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modified 3.7 years ago by Jorge Amigo ♦ 11k • written 3.7 years ago by L. A. Liggett • 120
1
gravatar for Jorge Amigo
3.7 years ago by
Jorge Amigo ♦ 11k
Santiago de Compostela, Spain
Jorge Amigo ♦ 11k wrote:

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.
ADD COMMENT • link written 3.7 years ago by Jorge Amigo ♦ 11k
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