Pipeline release! nf-core/sarek v3.8.1 - 3.8.1 - Laitaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.1
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Release 3.8.1 - Laitaure · nf-core/sarek
What's Changed
Fix bcftools concat on Strelka somatic VCFs by @FriederikeHanssen in #2128
Full Changelog: 3.8.0...3.8.1
GitHubPipeline release! nf-core/sarek v3.8.0 - 3.8.0 - Sitojaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.0
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/sarek v3.7.1 - 3.7.1 - Buollámtjåhkka!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.1
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Release 3.7.1 - Buollámtjåhkka · nf-core/sarek
What's Changed
Fix Haplotypecaller failure on 3.7.0 in #2069
Update modules: MultiQC (1.31 -> 1.33; adds BBsplit reporting) and BBSplit (bug on shared file systems)in #2073
Validate umi_read_struc...
GitHubPipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.0
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics
Release 3.7.0 - Saltoluokta · nf-core/sarek
What's Changed
New Tools
#2044 - Added VCF filtering with bcftools after variant calling
#2049 - Added consensus calling for small variants called by multiple tools (default: 2+ tools)
New Parame...
GitHub
Release Sarek 3.6.1 - Sjnjierák · nf-core/sarek
What's Changed
This release contains a fix for --aligner parabricks to use the correct intervals channel when running with --wes or --intervals <file> see #2029.
This patch release includes a bump ...
GitHub
Release Sarek 3.6.0 - Kvikkjokk · nf-core/sarek
What's Changed
Main new features
🧬 Lots of improvements around UMI support (#1937, @SPPearce)
⏩ Parabricks support (#1804, @famosab)
🔍 Muse (#1744, @famosab) and Sentieon TNScope (#1934, @SPPearc...
GitHub
Release 3.5.1 - Akkatjåkkå · nf-core/sarek
What's Changed
Changed
Bump schema version to 2.2.1 in #1767 by @FriederikeHanssen
Merge intervals for WES in GATK GenomicsDBImport in #1777 by @tdanhorn
Fixed
Use file-path-pattern over file-pa...
GitHub
Release 3.5.0 - Áhkájiegna · nf-core/sarek
What's Changed
Added
Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in #1620, #1653, #1752
Tool: Indexcov by @lindenb in #1613, #1752
Expose fastp parameter --length_required by @LouisLeNe...
GitHub