Fix IntegrateGQ.sh errors due to presence of variants of just one type #760
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mwalker174
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Jan 28, 2025
| @@ -30,41 +30,57 @@ zcat $RD_melted_genotypes \ | |||
| |gzip \ | |||
| >rd_indiv_geno.txt.gz | |||
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| ##Deletions, need to PE-SR genotypes to match RD format (2==ref)## | |||
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I think you should keep this comment in and the one about duplications below
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Updated accordingly.
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@mwalker174 Going to mark this as a draft PR until I've got more clarity into why some of the genotypes are being changed. I did take a quick look already, and it seems like the specific outputs from |
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This PR addresses Issue #759.
Description
Addresses an issue in the
IntegrateGQ.shscript where the combination ofset -o pipefail and{ fgrep ... || true; }patterns could cause pipelines to fail prematurely if no matches were found. By leveragingawkwithARGIND, the script no longer fails silently and continues processing regardless of theSVTYPEmakeup of the shard.Testing
Test 1: Changes circumvent WDL failure.
IntegrateGQ.sh, wherein each variant in its depth & PESR VCFs are of type- note that the run fails.IntegrateGQ.sh- note that the run completes successfully.Test 2: Changes do not change the existing logic.
IntegrateGQ.sh, including all types of variants.IntegrateGQ.sh- note that the output depth & PESR VCFs are identical.Test 3: Changes produce expected results when using DEL-only inputs.
Conducted local tests where I used the
IntegrateGQ.shinputs for a run that contained all variants, then removed all non-DEL records from this. After runningIntegrateGQ.shwith these DEL-only inputs, the outputs were identical for the matched counterparts in the case where the inputs contained all variants.Note: If it's preferred to reflect this in Terra, let me know - I did it locally for the time being as there is no dedicated WDL file to test
IntegrateGQin isolation, though I could make one.Test 4: Changes produce expected results when using only non-DEL inputs.
Same as Test 3, but this time removed all DEL records from the inputs. The outputs were identical for the matched counterparts in the case where the inputs contained all variants.