Bcftools mpileup

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
15/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Domain
bioinformatics

Research direction

Start with the reported bcftools mpileup command and its input settings; the issue does not include the command, options, or logs needed to investigate the 1.5 TB output. Reproduce the run with the 91 indexed BAM files and reference if those details can be obtained, then determine whether the output size is expected or indicates an error.

Written by the indexing model from the issue text.

Description

needs-feedback

I am using 91 bam files each of 500 mb size
Bam files sorted and indexed and reference maize genome is also indexed of 2.5 gb . Then i proceeded for bcftools mpileup for bcf file but the command is running from 2 days and file is growing to 1.5 tb So to estimate size if bcf or i want to to know this file size is fine or unusal or is there any error

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

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