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3 votes

dealing with a list of VEP files

For these requirements, it might be possible to simply use filter_vep included in the VEP package for this. Note that multiple --filter flags are ANDed together (i....
Steve's user avatar
  • 3,079
2 votes

How to calculate the variant allelic fraction (VAF) from VEP output?

If you just have a VEP output (i.e. VCF) without raw genotypes then you cannot calculate the allelic fraction.
user438383's user avatar
  • 1,679
2 votes

Error installing VEP on mac

You can try and get Perl's ExUtils::Builder, described here correctly installed and working, for example perl -MCPAN -e shell force install Bundle::CPAN You might ...
M__'s user avatar
  • 12.1k
1 vote
Accepted

Variants from multiple tools: normalization before or after annotation with VEP?

If you're referring to left alignment + parsimonious representation, do it before any annotation. Most if not all annotation happens by comparing CHROM, POS and optionally REF and ALT and since vt ...
Ram RS's user avatar
  • 2,279
1 vote
Accepted

VEP annotation INFO field Ensembl IDs and locations

You need to set your expectations clearly instead of just saying "Does not agree". I'm taking a guess here - your statement is that the 2/4 of the gene co-ordinates do not overlap the ...
Ram RS's user avatar
  • 2,279
1 vote

dealing with a list of VEP files

You don't need R or Python for this, it is a very straightforward text parsing problem and you can easily do it in an awk one-liner: ...
terdon's user avatar
  • 9,846
1 vote

Error installing VEP on mac

VEP requires gcc and g++ for installation1. Before running the build script, try setting the ...
Steve's user avatar
  • 3,079

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