I am filtering a VEP annotated vcf, trying to maintain just those variants classified as deleterious by
SIFTand as damaging (probably or possibly included) by
I am using:
filter_vep -i "$input" -o "$output" -filter "SIFT = deleterious and PolyPhen match damaging"
and I also tried:
filter_vep -i "$input" -o "$output" -filter "SIFT match deleterious and PolyPhen match damaging"
The output contains just variants with some value in these two fields, but some of the variants are classified as tolerated by
SIFT and as benign by
PolyPhen, so do you know why the filter is not working?
As an example: this two variants shouldn't exist in my filtered VCF, because the first one is classified as benign by PolyPhen and the second is classified as benign by both fields:
CHROM POS REF ALT FILTER INFO 1 1934441 . G T . PASS deleterious(0.01)|benign(0.138) 1 207085100 . G A . PASS tolerated(0.16)|benign(0.037)
As an example of a variant that has pass properly those filters:
CHROM POS REF ALT FILTER INFO 2 3938449 . T A . PASS deleterious(0.01)|probably damaging(0.67)
Those are 3 variants among those that I have in my filtered VCF, but I should be getting just those variants which are classified as deleterious and damaging by both SIFT and PolyPhen, as the third variant I've shown.