Implementation details: In the NPM-sample-QC reference implementation, the genome-wide sequencing coverage of non duplicated reads, non clipped bases, non overlapping bases, primary alignments, achieving a mapping quality of 20 or greater is derived from mosdepth v0.3.2. It is further narrowed down to the non gap regions of GRCh38 assembly, autosomes only using bedtools intersect. The median absolute deviation of the coverage is then calculated using datamash.
expluded -> excluded
Good to include the comment given below or remove the high quality from the description? The high quality reads also not part of the description in the proposed GHIF WGS QC document!
NPM-sample-qc implementation metric Genome coverage uniformity doesn't select high quality reads using mosdepth
It is critcal that the (BAM/CRAM) alignment files generated only from the illumina PF reads.
expluded -> excluded
Good to include the comment given below or remove the
high quality
from the description? Thehigh quality
reads also not part of the description in the proposed GHIF WGS QC document!Genome coverage uniformity
doesn't select high quality reads usingmosdepth