I am filtering my an annotation file resulting from VEP running over a vcf. My command line is this:
filter_vep -i "$input" -o "$output" -filter "SIFT = deleterious and PolyPhen match damaging"
What I pretend is to obtain just those variants classified as deleterious by SIFT and as damaging (probably or possibly damaging) by PolyPhen field. The problem is that, I am getting some variants in the filtered files which are tolerated (in SIFT field) and benign (in PolyPhen).
As an example: here you can see two variants that shouldn't pass the filters: the first one is classified as benign by PolyPhen and the second one is classified as benign by both algorithms.
CHROM POS REF ALT FILTER INFO 1 1934441 . G T . PASS CONTQ=93;DP=79;deleterious(0.01)|benign(0.138) 1 207085100 . G A . PASS CONTQ=93;DP=76;tolerated(0.16)|benign(0.037)
Does anybody know what am I doing wrong?