Genome coverage uniformity

• ID: mad_autosome_coverage
• Description: The median absolute deviation of sequencing coverage derived from short paired-end sequencing high quality, non duplicated reads, primary alignments, achieving a base quality score of 20 or greater (Phred scale) and mapping quality of 20 or greater, in autosomes non gap regions of GRCh38 assembly. Overlapping bases are counted only once. It is critical that the (BAM/CRAM) alignment files be readily marked for duplicated reads.
• Implementation details: In the NPM-sample-QC reference implementation, the genome-wide sequencing median absolute deviation coverage of the non gap regions of GRCh38 assembly, autosomes only using bedtools subtract, non duplicated reads, non overlapping bases, primary alignments, achieving a base quality of 20 or greater and mapping quality of 20 or greater is derived from GATK Picard’s CollectWgsMetrics, reporting the MAD_COVERAGE field.
• Type: Integer (eg. 4)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO dnaalnqc