merge paired-end sequencing

Question

[gubrins]

Heys,

I'm creating a pipeline to do the SNP calling of whole-genome sequencing for a non-model organism and I have a doubt regarding the merging of the paired-end data. When should it occur? I already did all the pipeline (quality filtering, mapping, sorting, remove duplicates, and SNP calling with GATK), but in GATK best practises I never saw anything about merging the paired-end files. Could you light me on this?

Thanks, Gabriel

[ATpoint]

The alignment takes care of the paired-end data, beyond that there should be no specific step. Is there a specific concern you have, do the reads overlap each other?

[gubrins]

Thanks for your reply, I think my reads don't overlap, I was just afraid I missed a step, as rad-seq's softwares (as ipyrad) does a merging in the final outputs. Then, if I aligned with bwa my pair-end data that's all I should have done? Thanks again!