Up: Component summary Function

VariantLiftover

This is analogous to the LiftOver component, but for VCF files. The variants in a VCF file are lifted from one build to another (e.g. hg18 --> b37). This might be useful for integrating (multi-sample) VCFs from various different build into the same variant recalibration process.

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
chain TextFile Mandatory The chain file used in convertion (e.g. hg18tob37.chain).
oldReference FASTA Mandatory The reference file of the old build.
newReference FASTA Mandatory The reference file of the new build. The accessory dictionary (.dict) file is used and must exist in the directory containing the fasta.
variants VCF Mandatory Variants to be lifted over.

Outputs

Name Type Description
calls VCF Lifted over variants. The variants will now have coordinates in the new build.

Parameters

Name Type Default Description
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.
memory string "2g" 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.
original boolean false The original locations will be included in the INFO field when set to true.

Test cases

Test case Parameters IN
chain
IN
oldReference
IN
newReference
IN
variants
OUT
calls
case1 properties chain oldReference newReference variants (expecting failure)

# Simple test of chain liftover,
memory=1g,
original=true


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