Up: Component summary Component

DuplicateMarker

This component performs marking of PCR duplicates using Picard.

Complete documentation:

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

Inputs

Name Type Mandatory Description
in BAM Mandatory Input BAM file. The file can be a single-sample or a merged multi-sample alignment file.

Outputs

Name Type Description
outBam BAM Duplicate marked alignment file.
outMetrics TextFile Duplicate information output file of Picard.

Parameters

Name Type Default Description
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.
options string "" Custom Picard parameters can be set in their native format. E.g. "ASSUME_SORTED=true".
picard string "" Path to Picard directory, e.g. "/opt/picard", which containg the picard.jar file. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the Picard directory.
remove boolean false Remove duplicates instead of only marking them.

Test cases

Test case Parameters IN
in
OUT
outBam
OUT
outMetrics
case1 properties in (missing) (missing)

memory=1g,
remove=true,
picard=/opt/share/picard-2.6/


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