I have a vcf file which contains information on allele depth (i.e. number of reads which map to the reference and alternate allele):
1 752566 . G A 68 . GG=0,69,68,69,849,556,849,490,556,849;DP=274;AC=1;AN=2 GT:AD:DP:GQ:PL:GG 0/1:1,2:3:19:41,0,19:19,25,0,25,95,50,95,41,50,95
I was wondering whether there is a way (using bcftools for example, rather than some home made script) to reduce the coverage of the vcf to a certain coverage, by removing ref and alt reads? I.e., take a file which has a mean coverage of 40x and reducing the mean coverage to 3x. Obviously I want the PL scores in the INFO field to be adjusted accordingly (hence why I'd rather something like bcftools does it, rather than a home made script).
EDIT: just to say, I don't have access to the original SAM/BAM files, so the action has to be done on the vcf.