AutoGenerateReadGroupsByName

Overview

Group: SAM/BAM

Adds read groups to a BAM file for a single sample by parsing the read names.

Will add one or more read groups by parsing the read names. The read names should be of the form:

<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<xpos>:<y-pos>

Each unique combination of <instrument>:<run number>:<flowcell ID>:<lane> will be its own read group. The ID of the read group will be an integer and the platform unit will be <flowcell-id>.<lane>.

The input is assumed to contain reads for one sample and library. Therefore, the sample and library must be given and will be applied to all read groups. Read groups will be replaced if present.

Two passes will be performed on the input: first to gather all the read groups, and second to write the output BAM file.

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
sample	s	String	The sample to insert into the read groups	Required	1
library	l	String	The library to insert into the read groups	Required	1
sequencing-center		String	The sequencing center from which the data originated	Optional	1
predicted-insert-size		Integer	Predicted median insert size, to insert into the read groups	Optional	1
program-group		String	Program group to insert into the read groups	Optional	1
platform-model		String	Platform model to insert into the groups (free-form text providing further details of the platform/technology used)	Optional	1
description		String	Description inserted into the read groups	Optional	1
run-date		Iso8601Date	Date the run was produced (ISO 8601: YYYY-MM-DD ), to insert into the read groups	Optional	1
comments		String	Comment(s) to include in the merged output file’s header.	Optional	Unlimited
sort-order		SamOrder	The sort order for the output sam/bam file.	Optional	1