BAM Quality Control

Overview

To evaluate the quality of a bam file, different metrics are calculated using the custom script bamqc.py.

The metrics currently available are:

• Mapping stats

  • Total reads
  • Reads with both mates mapped
  • Reads with one mate mapped
  • Reads with neither mate mapped

• Read length

• Coverage

Definitions

Mapping Statistics

The number of reads (not alignments) are counted as the number of unique read pairs (i.e., if a read pair is mapped to multiple locations it is only counted once).

Coverage

Coverage (=Depth of Coverage) is calculated as below:

{ (number of reads w/ both mates mapped) * (read length) * 2 + (number of reads w/ one mate mapped) * (read length) } / (effective genome size)

Here, the effective genome size is the number of non-N bases in the genome for WGS and an estimation of mappable space (exon and UTR regions) for WES.