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Clinical-Genomics-Lund / nextflow_wgs

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Overlapping inversions and deletions #188

Open ViktorHy opened 5 months ago

ViktorHy commented 5 months ago

In one case we had an inversion called from manta and tiddit.

In the same region there were also a deletion. This was called by GATK

GATK was the only caller for the del call, the inversion calls didnt not make it scout as we dont look at these. This caused the del to get penalties cause it was a short variant and thus it recieved low GQC,

see /data/bnf/dev/viktor/misc-scripts/github_issues/nextflow_wgs/188

ViktorHy commented 5 months ago

it should be noted that the inversion and deletion seems to be the same event, the exact mechanism is not understood completely but it causes manta and tiddit to miss the deletion. Both inversion and deletion are true positives