Merge speed has not been increased by '--threads' option ?

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#2,340 2 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
30/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
cli, performance

Research direction

Start by reproducing bcftools merge --file-list list.txt -O z -o output.vcf --threads 16 with the reported 200 VCF inputs, comparing CPU usage, virtual memory, and elapsed merge time. Trace how the merge command uses --threads and confirm whether the observed behavior is reproducible; document the result and any specific limitation found.

Written by the indexing model from the issue text.

Description

bcftools merge ---file-list list.txt -O z -o output.vcf --threads 16

Why the CPU% is only about 130%, but Virtual Memory has increased to 60G？
What‘s important is that the MERGE speed has not been increased！！！

（My file-list contains 200 samples with vcf.gz format. There are infomation of each site in those VCF files, not only variants site）

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

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