Illumina reads preprocessing best practice for snp calling applications

Question

[Denis]

Hi there,

I'm looking for the right strategy for preprocessing of raw reads for following snp calling. In particular, i'm thinking about running trimmomatic on the raw reads for trimming low quality reads position and adapter removal. Is it recommended step prior the snp calling?

Here: https://www.nature.com/articles/hdy2016102 was mentioned that trimming low quality reads position and adapter removal are necessary.

Are any other steps are required before the reads mapping to reference genome?

Answer 1

[Matthias Zepper]

Not before mapping, but you will want to recalibrate the quality and correct errors in your reads later to remap. BBTools has a basic preprocrocessing guide for variants that comes with the software and is contained in /docs/guides/CallVariantsGuide.txt. A bit more detailed is the GATK Best practices pipeline, which is also implemented in the Sarek pipeline. If you prefer Snakemake workflows, Varlociraptor might be for you. Oh, and pick the correct reference genome, as there are subtle but important differences.

[Denis]

Thank you for your reply and links you provided! They are very informative. It's interesting that according to the BBTools guide, adapter trimming is a recommended step for raw reads preprocessing and quality trimming is optional. But there is nothing about reads trimming in the GATK Best pactice pipeline. It seems that they used just raw reads for mapping to the reference.

[Enrique]

Hi! I'm still interested in the step that you use for the SNP calling. Did you use trimmomatic or another tool for trimming before mapping? Or just map and call the SNP without trimming? Thank you!