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PrepRnaBam

Preprocessing of RNA bam files according to GATK best practices (adding groups, marking duplicates, splitNtrim and base recalibration)

Version 1.0
Bundle sequencing
Categories Alignment
Authors Amjad Alkodsi (amjad.alkodsi@helsinki.fi)
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Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
reference FASTA Mandatory The reference fasta file.
in BAM Mandatory Input BAM file.
dbsnp VCF Mandatory File with known SNPs to mask, usually from latest dbSNP distribution. The file is used in GATK to improve base quality calibration.
mask VCF Optional File with known sites to mask. This will be used exactly as 'dbsnp'.

Outputs

Name Type Description
alignment BAM Final preprocessed bam file.
markReport BinaryFile The report file created by picard during marking duplicates.
recalReport GatkReport The report file created in the first step and used in the second step of recalibration.

Parameters

Name Type Default Description
ID string "1" Read group ID.
LB string "library1" Read group library.
PL string "ILLUMINA" Read group platform.
PU string "Unit1" Read group platform unit.
SM string "Sample1" Read group sample name.
gatkPath string "" Path to GATK directory containing the 'GenomeAnalysisTK.jar'. If empty string is given (default), GATK_HOME environment variable is assumed to point to the GATK directory where GenomeAnalysisTK.jar is located.
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.
picardPath string "" Path to Picard directory, e.g. "/opt/picard", which containg the Picard-tools. If empty PICARD_HOME is used

Test cases

Test case Parameters IN
reference
IN
in
IN
dbsnp
IN
mask
OUT
alignment
OUT
markReport
OUT
recalReport
case1 properties reference in dbsnp (missing) (missing) (missing) (missing)

ID=ID2


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