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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 PolyPhen.

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.

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    $\begingroup$ Please edit your question and add a minimal VCF file that we can use to reproduce your issue. Make sure to include the necessary headers (and only the necessary ones), at least one variant that should pass, one variant that should fail and then show us what output you expect from this example and what output you're actually getting. We cannot help you debug a problem if you don't show what you are trying to parse. $\endgroup$ – terdon May 3 at 14:52
  • $\begingroup$ @terdon Okay, I've included those things $\endgroup$ – Jeni May 12 at 8:00
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If you are working under a Linux environment, then you may easily use a piped grep search. For example:

grep deleterious file.vcf |grep damaging >filtered_file.vcf
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