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.