bcftools mpileup for a set of Illumina+HiFi reads

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
20/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Quiet
Domain
bioinformatics

Research direction

The issue asks whether PacBio HiFi mpileup parameters are appropriate for mixed Illumina short-read and HiFi BAM files in joint genotyping. No source file, test, implementation target, or completion criterion is mentioned, so clarification and project guidance are needed before work can start.

Written by the indexing model from the issue text.

Description

I have a set of 100 short read bam and 50 long read animal bam files. I want to do joint-genotyping. Would it make sense to run mpileup using pacbio hifi parameters for both? I couldn't find such a scenario in the issues section. We are looking at pop gen analysis downstream.

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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