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Uploading more RNA tracks to a case for more individuals than there are DNA samples already #5310

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dnil opened this issue Mar 12, 2025 · 1 comment · May be fixed by #5327
Open

Uploading more RNA tracks to a case for more individuals than there are DNA samples already #5310

dnil opened this issue Mar 12, 2025 · 1 comment · May be fixed by #5327
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dnil commented Mar 12, 2025

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.
When updating a DNA case with RNA from a larger family, DROP/WTS filtering does not work. Compare enableddragon for upload to engagingmongrel.
@dnil dnil self-assigned this Mar 13, 2025
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dnil commented Mar 14, 2025 •
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It is really a bit involved. Adding extra "RNA" individuals is blocked by the DNA VCF not having the extra inds (and case integrity checks due to that). We should try to make sure we can have "pure" WTS individuals that are then not expected in DNA WGS/WES VCFs.

This particular case was solved by removing the extra individual. A pure WTS case could also be made.

grep -v NN2 enableddragon_outrider_top_hits_clinical.tsv > enableddragon_outrider_top_hits_clinical.no_NN2.tsv
grep -v NN2 enableddragon_fraser_top_hits_clinical.tsv > enableddragon_fraser_top_hits_clinical.no_NN2.tsv
...updating omics_files paths
...updating the individual id, and loading
scout update individual -c engagingmongrel -n family_number_3 omics_sample_id NN1
scout load variants --outlier engagingmongrel

dnil added a commit that referenced this issue Mar 14, 2025
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Partially fix #5310 - allow loading of mixed cases with some fully wt…
7252597 
…s sample individuals
@dnil dnil linked a pull request Mar 14, 2025 that will close this issue
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