FilterBam

Overview

Group: SAM/BAM

Filters reads out of a BAM file. Removes reads that may not be useful in downstream processing or visualization. By default will remove unmapped reads, reads with MAPQ=0, reads marked as secondary alignments, reads marked as duplicates, and if a set of Intervals are provided, reads that do not overlap any of the intervals.

If --min-insert-size or --min-mapped-bases is specified, unmapped reads will also be removed even if --remove-unmapped-reads is false.

NOTE: this will usually produce a BAM file in which some mate-pairs are orphaned (i.e. read 1 or read 2 is included, but not both), but does not update any flag fields.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input BAM file.	Required	1
output	o	PathToBam	Output BAM file.	Required	1
intervals	l	PathToIntervals	Optionally remove reads not overlapping intervals.	Optional	1
remove-duplicates	D	Boolean	If true remove all reads that are marked as duplicates.	Optional	1	true
remove-unmapped-reads	U	Boolean	Remove all unmapped reads.	Optional	1	true
min-map-q	M	Int	Remove all mapped reads with MAPQ lower than this number.	Optional	1	1
remove-single-end-mappings	P	Boolean	Removes non-PE reads and any read whose mate pair is unmapped.	Optional	1	false
remove-secondary-alignments	S	Boolean	Remove all reads marked as secondary alignments.	Optional	1	true
min-insert-size		Int	Remove all reads with insert size < this value.	Optional	1
max-insert-size		Int	Remove all reads with insert size > this value.	Optional	1
min-mapped-bases	m	Int	Remove reads with fewer than this many mapped bases.	Optional	1