populationgenomics / talos

Rare Disease variant reanalysis tool
MIT License
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Runtime Failures on CNV processing #421

Closed MattWellie closed 3 months ago

MattWellie commented 3 months ago

The new PED generation script has not been sequencing-type specific

When we gather all the relevant sample IDs, if a participant has an exome and a genome, the ped will only retain one.

This has lead to issues where the SV MTs are being processed and no overlap is found between the pedigree and MT/VCF

This runtime bug masks the deeper issue of 'some samples are arbitrarily being excluded from the analysis because they have a genome sample, and this is an exome run', or vice versa

Suggestion - limit the PED generation to exome or genome as appropriate. Delete the latest runs and regenerate