Up: Component summary Function

VariantCombiner

This function combines all input variant files into one file using the Genome Analysis Toolkit (GATK).

Complete documentation:

Version 1.0
Bundle sequencing
Categories VariationAnalysis
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 Reference fasta file.
variants Array<VCF> Optional Input VCF files
variants1 VCF Optional Input VCF file. For more than 5 files you can use the 'files' parameter for paths or use the combiner multiple times.
variants2 VCF Optional Input VCF file.
variants3 VCF Optional Input VCF file.
variants4 VCF Optional Input VCF file.
variants5 VCF Optional Input VCF file.

Outputs

Name Type Description
calls VCF Merged vcf file.

Parameters

Name Type Default Description
disjoint boolean false This will allow simple concatenation and considerably reduce the runtime for files with identical sample sets and disjoint calls (e.g. split chromosomes from the same patient).
files string "" A "-V"-tag separated list of paths to multiple variant vcf files (single- or multi-sample), e.g. files="-V FILE1.vcf -V FILE2.vcf, ... -V FILEN.vcf".
gatk string "" Path to GATK directory containing the 'GenomeAnalysisTK.jar' file. If empty string is given (default), GATK_HOME environment variable is assumed to point to the GATK directory where GenomeAnalysisTK.jar is located.
genotype string "UNSORTED" Defines how colliding variants are handled. Allowed values: {UNIQUIFY, PRIORITIZE, UNSORTED, REQUIRE_UNIQUE}
memory string "4g" The amount of java-heap memory being allocated to the GATK thread, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc.
options string "" This string will be added to the command and can include any number of options in the software specific format.

Test cases

Test case Parameters IN
reference
IN
variants
IN
variants1
IN
variants2
IN
variants3
IN
variants4
IN
variants5
OUT
calls
case1 properties reference (missing) variants1 variants2 (missing) (missing) (missing) (missing)

# Combines two variant files,
disjoint=false,
memory=1g,
genotype=UNIQUIFY


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