Should your variant calling pipeline change depending on whether using WES or WGS?

Question

[amy__]

Hi,

This might be an obvious question, but can you use the same pipeline for WES and WGS? They should all be in FASTQ file, but I just wanted to ask incase I was missing some basic biology between them.

Thanks! Amy

Answer 1

[Eugene A]

The main (and as far as I know the only) difference is the usage of different interval lists along your pipelinie for calling and QC metrics collection. but the tools essentially the same

[amy__]

Perfect, thank you so much!