confused by rs4124874 and rs12777823 variants

[mathob]

• Do you want to request a feature or report a bug?

bug

• What is the current behavior?

pharmcat_positions_0.8.0.fixed.vcf includes two deletion variants whose representation seems contrary to what is spefified for Deletions on the "VCF Requirements" page

• If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar.

java -cp pharmcat-0.8.0-all.jar org.pharmgkb.pharmcat.definition.ExtractPositions -o pgx.vcf cat pgx.vcf | grep -e rs4124874 -e rs12777823 chr2 233757013 rs4124874 T . . PASS PX=UGT1A1:*1[5]isT GT 0/0 chr10 94645745 rs12777823 G . . PASS POI GT 0/0

• What is the expected behavior?

variants representation with ALT allele not a dot ??

• What is the motivation / use case for changing the behavior?

testing PharmCat and wishing to understand messages warning of "missing" variants

• Please tell us about your environment:

  • PharmCAT Version: 0.8.0
  • JDK Version: java version "1.8.0_221"
  • Environment: macOS

• Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)

[mathob]

forget this please - sorry to bother you

[whaleyr]

No worries, this is actually a good question.

You may have already seen but rs4124874 has recenlty been removed from the UGT1A1 translation on the development branch so it won't be a position reported in future versions.

rs12777823 is what we consider an "extra" position. It's not actually used when matching defined haplotypes but it is a position that curators feel should be included when reporting genotypes. Since it's not used in a haplotype definition we don't have an "ALT" that we expect for that position, and that's what we use to determine what goes in the ALT for that file.

I hope that clarifies things a bit.

[mathob]

Yes, that all makes sense - thanks for taking thetime to reply, Ryan.

On 23 Apr 2021, at 3:47 am, Ryan Whaley @.**@.>> wrote:

No worries, this is actually a good question.

You may have already seen but rs4124874 has recenlty been removed from the UGT1A1 translation on the development branch so it won't be a position reported in future versions.

rs12777823 is what we consider an "extra" position. It's not actually used when matching defined haplotypes but it is a position that curators feel should be included when reporting genotypes. Since it's not used in a haplotype definition we don't have an "ALT" that we expect for that position, and that's what we use to determine what goes in the ALT for that file.

I hope that clarifies things a bit.

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