filter_vep not properly filtering

Question

[jeni]

Hi!

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?

[benformatics]

Why are you using '= delterious' and then 'match damaging' ... I would imagine the system requires some consistency?

[jeni]

Actually I have also used: ' match deleterious and match damaging', but I got the same result. The reason why I first used this is because PolyPhen can classify as possibly or probably damaging, and I wanted to include both classifications, while SIFT always classifies as deleterious when it is deleterious.