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Exome-seq Pipeline

This pipeline offers a end-to-end workflow for exome analysis using several toolchains

• trimming with fastp

• short read alignment using BWA, BWA2 or Dragmap

• duplicate marking using Samtools

• germline SNP/INDEL calling with Deepvariant, Strelka and/or GATK

• somatic SNP/INDEL calling with Mutect2 and Strelka

• variant effect prediction with VEP and/or Haplosaurus

• protein-level effect prediction with Haplosaurus and BCFtools

• germline and somatic SV calling using Manta

• germline and somatic CNV calling using CNVkit

• Repeat expansion detection using ExpansionHunter

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
6. Developer guide

Benchmarking

Benchmarking of release 4.3 against genome-in-a-bottle NA12878

DeepVariant

IDT xGEN, in-house:

Variant	Recall	Precision
Indel	0.92	0.98
SNP	0.994	0.999

Agilent v7, external:

Variant	Recall	Precision
Indel	0.93	0.97
SNP	0.99	0.998