analysis piplines for wes and wgs

Question

[l.eit]

Hi,

I would like to know if the analysis pipelines for wes and wgs are the same ? and if the same tools can be used in both cases?

By the analysis pipeline i mean the quality control, preprocessing of quality reads, alignment of reads to reference genome or denovo genome assembly, post alignment processing, variant calling and annotation.

Thanks!

Answer 1

[WouterDeCoster]

I don't think there are any notable differences, besides that with exome sequencing data you cannot do a sensible de novo "genome" assembly, but that is probably obvious.

Some recommended reading is the GATK Best Practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence

But I wonder why you ask this question, what you "actually" are looking for. Or simply a question out of curiosity?

[James Denvir]

Some structural variants can be difficult/impossible to call from WES data; but for "small" variants (SNPs and small indels) we have always used the same pipelines. Obviously WES needs less computing power than WGS.

[l.eit]

thanks for your answer, yes a question out of curiosity. I have learned about wgs analysis pipleines by myself and wanted to make sure that all of this can be applied to wes too, except the assembly point. thanks for the link too.