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nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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 (589 stars)
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 (539 forks)
Indexed issues
 (6 indexed issues)
open beginner issues
 (6 open beginner issues)
Latest indexed
Aug 13, 2026
Last GitHub push
Jul 30, 2026
License
MIT License
Contributing guide
Contributing guide
Code of conduct
Code of conduct
Dominant language
Nextflow
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Beginner labels
help wantedgood first issue

Issues

6 open indexed issues

Open
Enable Mutect2 force-calling using --alleles flag
enhancementgood first issue
Why recommendedNo assignee yet · No comments yet
No assignee yetNo comments yetHas a beginner-friendly labelRepository active this monthContributing guide available

nf-core / sarek · #1883 · May 2, 2025 · Nextflow · 589 stars

0 comments0 reactions0 assignees
Open
Tutorial: CNV calling
enhancementhelp wanted
Why recommendedNo assignee yet · No comments yet
No assignee yetNo comments yetHas a beginner-friendly labelRepository active this monthContributing guide available

nf-core / sarek · #1713 · Oct 30, 2024 · Nextflow · 589 stars

0 comments0 reactions0 assignees
Open
Proposals for Sarek Tutorials on use-cases
docshelp wantedtesting
Why recommendedNo assignee yet · Has a beginner-friendly label
No assignee yetHas a beginner-friendly labelRepository active this monthContributing guide available

nf-core / sarek · #1704 · Oct 28, 2024 · Nextflow · 589 stars

3 comments2 reactions0 assignees
Open
Get a full nf-test report in cis
enhancementhelp wanted
Why recommendedNo assignee yet · No comments yet
No assignee yetNo comments yetHas a beginner-friendly labelRepository active this monthContributing guide available

nf-core / sarek · #1699 · Oct 28, 2024 · Nextflow · 589 stars

0 comments0 reactions0 assignees
Open
joint genotyping optimal strategy
help wanted
Why recommendedNo assignee yet · Has a beginner-friendly label
No assignee yetHas a beginner-friendly labelRepository active this monthContributing guide available

nf-core / sarek · #923 · Jan 25, 2023 · Nextflow · 589 stars

1 comment0 reactions0 assignees