DownsampleAndNormalizeBam

Overview

Group: SAM/BAM

Downsamples a BAM in a biased way to a uniform coverage across regions.

Attempts to downsample a BAM such that every base in the genome (or in the target regions if provided) is covered by at least coverage reads. When computing coverage:

• Reads marked as secondary, duplicate or unmapped are not used
• A base can receive coverage from only one read with the same queryname (i.e. mate overlaps are not counted)
• Coverage is counted if a read spans a base, even if that base is deleted in the read

Reads are first sorted into a random order (by hashing read names). Reads are then consumed one template at a time, and if any read adds coverage to base that is under the target coverage, all reads (including secondary, unmapped, etc.) for that template are emitted into the output.

Given the procedure used for downsampling, it is likely the output BAM will have coverage up to 2X the requested coverage at regions in the input BAM that are i) well covered and ii) are close to regions that are poorly covered.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input SAM or BAM file.	Required	1
output	o	PathToBam	Output SAM or BAM file.	Required	1
coverage	c	Int	Desired minimum coverage.	Required	1
min-map-q	m	Int	Minimum mapping quality to count a read as covering.	Optional	1	0
seed	s	Int	Random seed to use when randomizing order of reads/templates.	Optional	1	42
regions	l	PathToIntervals	Optional set of regions for coverage targeting.	Optional	1
max-in-memory	M	Int	Maximum records to be held in memory while sorting.	Optional	1	1000000