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
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