Ploidy restrictions in norm and csq
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 30/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the trisomy-X case with a genotype represented as 0/1/1, then inspect the implementations and tests for the bcftools norm and csq commands. Determine where ploidy is restricted and assess the implications for both commands. Done means ploidy-three records work correctly in norm and csq without regressing existing diploid behavior.
Written by the indexing model from the issue text.
Description
When splitting multiallelics using bcftools norm in one of our cohorts it fails on reaching the X chromosome because we have an individual with trisomy X in there, which we have called appropriately for the X chromosome using GATKs HaplotypeCaller ie the genotypes are represent in the form 0/1/1 for the trisomic X chromosome. We would really like to keep this individual, and any other sex chromosome aneusomies that we might find, represented appropriately in our cohort as it may well be relevant to the biology of the disease. Is it possible to increase the ploidy allowed to three?
Similarly we are finding bcftools csq very useful and it also fails when the ploidy is 3 - probably a more difficult problem to address, but any possibility?
Thanks
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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