Releases: TRON-Bioinformatics/covigator-ngs-pipeline
Releases · TRON-Bioinformatics/covigator-ngs-pipeline
Release Covigator NGS pipeline v0.3.0
Major changes
- Add read trimming with fastp
- Output QC results in JSON format
- Integrate 4 variants callers: BCFtools, iVar, GATK and LoFreq
- Include soft filtering of variants based on VAF for all variants from LoFreq and for indels from BCFtools
- Integrate SnpEff 5.0 for the variant annotation
- Parametrize some quality thresholds
Covigator NGS pipeline v0.2.0 BETA
First pre-release integrating alignment, mark duplicates, realignment around indels, variant calling with samtools, variant normalization and variant annotations with bcftools csq.