Up: Component summary Component

GetReads

Visualizes reads that are aligned to a given position.

Version 1.0
Bundle sequencing
Categories
Authors Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker View/Report issues
Requires picard-1.62.jar (jar) ; sam-1.32.jar (jar) ; installer (bash)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
alignment BAM Optional A bam or sam file
array Array<BAM> Optional An array of bam or sam files

Outputs

Name Type Description
reads TextFile Reads in the given position

Parameters

Name Type Default Description
chromosome string (no default)
position int (no default)

Test cases

Test case Parameters IN
alignment
IN
array
OUT
reads
case1 properties alignment (missing) reads

chromosome=chr21,
position=33045397

case2 properties (missing) array (missing)

chromosome=chr21,
position=33045359

case3 properties alignment (missing) reads

chromosome=chr21,
position=33045404


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