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seqan / iGenVar

The official repository for the iGenVar project.
BSD 3-Clause "New" or "Revised" License
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[FIX,BENCHMARK] Split input files into GRCh37 and GRCh38 #204

Closed Irallia closed 2 years ago

Irallia commented 2 years ago

Resolves #203

I have noticed that our benchmark files are not all from the same version of the human genome. Some are from GRCh37 (hg19) some are from GRCh38 (hg38). Since GRCh38 is the newer version, I tried to change everything to this, but failed at the truth set. This is only available for GRCh37. There are tools with which one can carry out a coordinates conversion, e.g. from 37 to 38. For the 10xGenomix BAM file this worked and also for the bed file. But for the vcf I could not do it. I have therefore left all code for this in the scripts and would use GRCh37 until there is a truth set for 38.

codecov[bot] commented 2 years ago

Codecov Report

Merging #204 (c1e015a) into master (df85b78) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #204   +/-   ##
=======================================
  Coverage   98.35%   98.35%           
=======================================
  Files          18       18           
  Lines         850      850           
=======================================
  Hits          836      836           
  Misses         14       14

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