How to process Bulk WES data?

Question

[wyuan37]

I am new to BULK data and I am wondering how is this different from process scDNA-seq data. Does anyone know a pipeline for that? Normally, the scDNA-seq process starts with the alignment, coordination sort, mark duplication, and removal of those. Can I use the same pipeline for processing the Bulk WES data?

[GenoMax]

You could use sarek (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2