Up: Component summary Function

BamRegrouper

Picard-tools is used to add or replace read group information for each read in the input alignment file. This might be required for files that have faulty information and fail the calling procedure, which heavily uses read group information.

Version 1.0
Bundle sequencing
Categories Alignment
Authors Rony Lindell (rony.lindell@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
bam BAM Mandatory Input BAM file.

Outputs

Name Type Description
alignment BAM Final bam file with read groups replaced.

Parameters

Name Type Default Description
ID string "1" Read group ID.
LB string (no default) Read group library.
PL string (no default) Read group platform.
PU string (no default) Read group platform unit.
SM string (no default) Read group sample name.
memory string "4g" The amount of java-heap memory being allocated to each GATK and Picard thread, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc.
picard string "" Path to Picard directory, e.g. "/opt/picard", which containg the Picard-tools .jar files. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the Picard directory.

Test cases

Test case Parameters IN
bam
OUT
alignment
case1 properties bam (missing)

# Default run using less memory,
memory=1g,
ID=foo,
LB=bar,
PL=platform,
PU=barcode,
SM=sammy


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