Up: Component summary Component

SubsetBam

Extracts reads from a BAM file based on chromosomal regions specified by a user and produces a merged BAM file containing only those regions.

For example, this component can be used to subset a BAM file to contain only those reads which map to genes of interest.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
Issue tracker View/Report issues
Requires samtools ; csvkit
Source files component.xml SubsetBam.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
in BAM Mandatory Input sorted and indexed BAM file.
annotation CSV Mandatory DNARegions which are used for subsetting. Locus information can be either in the DNARegion format ('chr:start-end') or as separate columns 'chr,start,end'. Set 'chrCol' parameter accordingly.

Outputs

Name Type Description
out BAM Subsetted BAM file.

Parameters

Name Type Default Description
chrCol string "chr,start,end" Column name or names for annotation input. If the locus information is on multiple columns, this parameter needs to be a comma-separated list of column names in 'annotation'. Otherwise, the name of the DNARegion formatted column in 'annotation'.

Test cases

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

chrCol=chr,start,end

case2 properties (missing) annotation (missing)

chrCol=chr:start-end


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