mhoeppner/exome-seq repository overview

⁠Exome-seq Pipeline

This pipeline offers a end-to-end workflow for exome analysis using the GATK4 toolchain

• trimming with Fastp
• read alignment with BWA
• duplicate marking using Picard MarkDuplicates
• quality score recalibration
• gvcf calling
• joint variant calling -- variant hard-filtering [default] -- variant recalibration (SNPs and Indels) and filtering [optional, off by default and only recommended for >= 30 exomes]

The result will be a multi-sample VCF file as well as a list of VCF files for each sample.

⁠Documentation

1. What happens in this pipeline?⁠
2. Installation and configuration⁠
3. Running the pipeline⁠
4. Output⁠
5. Troubleshooting⁠