Hi, I use Freebayes as variant caller and I usually use vcftools to perform hard filtering of variants based on minimum depth values.
So for example, if any sample has a value of less than 8 reads (DP), the GT is not taken into account.
An example of the output (after using vcf-query) is:
SNP REF ALT GT RO/AO DP SNP1 A T A/A 10/0 10 SNP2 T G T/G 20/40 60 SNP3 C G C/C 15/0 15 SNP4 T G G/G 0/9 9 SNP5 A G ./. 2/3 5
The command I use is
vcftools --gzvcf input.vcf.gz --minDP 8 --recode --recode-INFO-all --out output which let me modify the GT call based on the DP value.
My main problem, is that vcftools doesn't support polyploids for this type of filtering. Is there a similar function in bcftools. If so, I cannot find it.