ga4gh/quality-control-wgs metrics_definitions.md - Mean autosome coverage

[justinjj24]

Description: The mean sequencing coverage derived from short paired-end sequencing high quality, non duplicated reads, primary alignments, achieving a mapping quality of 20 or greater, in autosomes non gap regions of GRCh38 assembly. Clipped bases are expluded.

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 Mean autosome coverage doesn't select high quality reads using mosdepth
• It is critcal that the (BAM/CRAM) alignment files generated only from the illumina PF reads.

[justinjj24]

no we keep the mention of high quality reads ... even if indeed there hasn'nt been any NGS delivered with non PF PASS for 10+ years.

@mhebrard please take note of the typo also informed of the typo in https://github.com/ga4gh/quality-control-wgs/issues/9#issuecomment-1504602516