Up: Component summary Function

BamReorder

This function reorders reads in a BAM file to match the contig ordering in the provided reference file.

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
reference FASTA Mandatory The reference fasta file.
bam BAM Mandatory Input BAM file.

Outputs

Name Type Description
alignment BAM Final reordered bam file.

Parameters

Name Type Default Description
incomplete boolean false Allow an incomplete overlap of input bam file contigs with the reference contigs.
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
reference
IN
bam
OUT
alignment
case1 properties reference bam (missing)

# Default run using less memory,
memory=1g,
incomplete=true


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