bcftools DP filtering and recode as vcftools, but for polyploids?

Question

[dfajar2]

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.

Thanks

Answer 1

[finswimmer]

The bcftools plugin setGT might help you here:

bcftools +setGT input.vcf -- -t q -n . -i 'FORMAT/DP<8'

This would set any genotype to ./. for samples with DP<8

fin swimmer

[dfajar2]

Thanks!! I didn't knew about the plugins!!! It worked great.

[Ram]

Glad finswimmer's solution worked for you, dfajar2. I've moved it to an answer. Please click on the green check mark to mark your question as resolved.