ikmb/exome-seq repository overview

⁠Exome-seq Pipeline

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

• trimming with Fastp

• read alignment with BWA

• duplicate marking using Samtools

• vcf/gvcf calling with Deepvariant

• joint variant calling with GLNexus

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