How to populate Fisher test annotation
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reviewing the linked discussion in issue #1834 and the mpileup behavior described here. Determine whether FS can be populated from the retained forward/reverse read-depth values without recalling genotypes, and identify the code or documentation needed to provide a supported answer.
Written by the indexing model from the issue text.
Description
Hello, I'm revisiting this comment as I've run into a similar observation in my dataset- the FS field (fisher test for strand bias) does not seem to be correctly populated — it is coming up as zero for all genotypes so everything is passing. I've read through this thread and am a bit confused- is this something that needs to be explicitly specified (ie, accounting for this is not the default)?
We've just spent a long time calling reads for a very large dataset and would like to avoid doing it all over again. Is there a way to populate this field after the bcftools mpileup? We have retained the read depth for for/rev reads supporting alt/ref so is it possible to calculate this without recalling genotypes? Thank you so much!
Originally posted by @paigeduffin in https://github.com/samtools/bcftools/issues/1834#issuecomment-2354477466
- Dominant language
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