Up: Component summary Component

Bam2Fastq

Revert BAM file to Fastq file for realignment. Requires Samtools and Picard to run from PATH.

Version 0.1
Bundle sequencing
Categories Convert smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi)
Issue tracker View/Report issues
Requires samtools ; picard ; installer (bash)
Source files component.xml Bam2Fastq.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
in BAM Mandatory Input BAM alignment file.

Outputs

Name Type Description
out FASTQ Output FASTQ file.

Parameters

Name Type Default Description
picard string "../../lib/picard-tools-1.131" Path to picard installation.

Test cases

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

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