Recent Releases of vcftocounts
vcftocounts - 2.0.1 - Pipe Cerulean
What's Changed
- fix: use whole name instead of baseName for gvcf to vcf by @famosab in https://github.com/qbic-pipelines/vcftocounts/pull/29
- fix: use filtered vcfs for subsequent processes by @famosab in https://github.com/qbic-pipelines/vcftocounts/pull/30
Full Changelog: https://github.com/qbic-pipelines/vcftocounts/compare/2.0.0...2.0.1
- Nextflow
Published by famosab about 1 year ago
vcftocounts - 2.0.0 - Rad Sepia
Initial release of (renamed) qbic-pipelines/vcftocounts.
Changed
- #25 - Rename pipeline to vcftocounts + Prepare Release 2.0.0
- #28 - Move test data to test-datasets, create filter nf-test
Added
- #22 - Remove ID column entries from VCFs
- #23 - Add filtering of VEP annotated VCF files using bcftools/view (no conda for NXF_VER <= 24.10.2)
Fixed
- #15 - template update to v3.1.1
- #16 - Fix bcftools/reheader bug
- #21 - template update to v3.2.0
- #24 - Change branching logic to enable caching again + rename vcf2mat to vcf2counts (thank you @awgymer for helping)
- Nextflow
Published by famosab over 1 year ago
vcftocounts - 1.0.0 - Curie Purpureal
This is the initial release of a pipeline that can take (g)VCF files and converts them a table format useful for statistical analysis.
- Indexes (g.)vcf files (tabix)
- Converts g.vcf files to vcf with genotypegvcf (GATK)
- Merges all vcfs from the same sample with bcftools/merge (bcftools)
- Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro (R)
- Collects all reports into a MultiQC report (MultiQC)
- Nextflow
Published by famosab over 1 year ago