I have a very general question. Does anybody have advices, guidelines, papers, softwares 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 :
and also some tracks with samtools (flagstat, depth,...) and bedtools (coverageBed, intersectBed,...)
Thanks for your advices!