Hello, I've called genotypes using samtools/bcftools and am now trying to filter the genotype calls based on mean depth (DP > 10). However, when I use the
minDP filter in vcftools nothing happens. Alternately, the
minQ filter seems to be working well. Any ideas why this is or what I could do?
Here's the command I am trying to use:
vcftools --gzvcf my_file.vcf.gz --minQ 30 --minDP 10 --recode-INFO-all --recode --out filtered.
In case it helps, here is a few sites from my pre-filtered VCF. Thanks!
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample > chr1 864 . C G 9.6787 . DP=1 GT:PL 0/1:27,3,0 > chr1 11322 . A G 11.5001 . DP=1 GT:PL 0/1:29,3,0 > chr1 22289 . G T 180 . DP=56 GT:PL 1/1:197,169,0
There's some other information for each site under info (e.g.
;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=60) which I've removed from this example to keep everything more clean.