Hello everyone!

I have a very general question. Does anybody have advice, guidelines, papers, software about good practice for clinical NGS data pipelines?

My aim is to set up a quality process for my lab using a home made build pipeline or something already existing.

What I have in mind (but definitely not sufficient) : analysis and control (log files during all the process) of data generated from sequencing and post-sequencing analysis (vcf, contigs files...) and also generation of a clear and synthetic report

I found these valued articles:

• Good laboratory practice for clinical next-generation sequencing informatics pipelines (Nat Biotechnol. 2015)

• Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests (J Pathol Transl Med. 2017)

  and also some tracks with samtools (flagstat, depth,...) and bedtools (coverageBed, intersectBed,...)

Thanks for your advice!