BAM Quality Control

Overview

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

The metrics currently available are:

• mapping stats - total reads - reads w/ both mates mapped - reads w/ one mate mapped - reads w/ neither mate mapped
• read length
• coverage

Definitions

Mapping stats

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

where effective genome size is the number of non-N bases in the genome.