How to use BCFtools to keep variants if they are `DP > 10` in all samples?

Question

[K.patel5]

Dear Biostars,

To clarify this question is about best practices with trio-samples (proband, mother, father). I have been able to remove low confidence variants from .vcf.gz files via:

bcftools filter -Oz -i'FMT/DP>10' ${path}/x.vcf.gz > ${path}/x_filt.vcf.gz

This removes variants where the DP is less than 10 all three samples. However, this keeps variants where one sample has more than 10 reads, and the others do not. Below are two lines from x_filt.vcf.gz:

Format            Pband                  Mother                   Father
GT:AD:DP:GQ:PL    0/0:5,0:5:15:0,15,209  0/1:9,12:21:99:438,0,342 0/0:2,0:2:6:0,6,84
GT:AD:DP:GQ:PL    0/0:6,0:6:15:0,15,225  0/1:8,5:13:99:186,0,300  1/1:0,2:2:6:90,6,0 

The DP is <10 in the Proband and Father for both variants, but passes the filtration due to the Mother having DP >10.

How can I remove cases such as these? Preferably using BCFtools, however other suggestions are welcome.

Many Thanks, Krutik

[cpad0112]

can you try filter by MIN(DP)>10

Answer 1

[Pierre Lindenbaum]

(not tested)

 bcftools view -i 'MIN(FORMAT/DP)>10' 

[K.patel5]

Thanks, that did the trick.