bcftools add AD column

Question

[martina.gallinaro]

Hi everyone.

I would like to add to the vcf file that I obtained with samtools mpileup the field AD. I did the following command:

samtools mpileup -A -d 6000 -B -C 50 -g -f $ref  -s $input.bam | bcftools call -mv -Oz -o $output.vcf 

In my vcf file I had these informations in the INFO field:

DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=39

I would like to have also AD field. Can anyone help me? Thank you!!

Answer 1

[Pierre Lindenbaum]

bcftools mpileup  -a 'INFO/AD' (...)