Up: Component summary Component

BamCombiner

Merges multiple bam files using the Picard MergeSamFiles. The output bam is a dynamically merged and coordinate sorted bam file.

Version 2.0
Bundle sequencing
Categories Alignment
Authors Amjad Alkodsi (amjad.alkodsi@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml bamCombiner.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
in Array<BAM> Mandatory Array of bam files.

Outputs

Name Type Description
out BAM The merged alignment bam file.

Parameters

Name Type Default Description
memory string "4g" The amount of java-heap memory being allocated to PICARD, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc.
options string "" Additional MergeSamFiles arguments can be set here.
picard string "" Path to picard directory. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the GATK directory.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in (missing)

memory=1g


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