Up: Component summary Function

VariantValidator

This function validates the input variant file using the Genome Analysis Toolkit (GATK). Malformated files or files with misinformation will give errors. Applying a dbSNP file will also check concordance of dbSNP ID annotations.

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 The reference fasta file.
variants VCF Mandatory Input variants.
dbsnp VCF Optional File with known SNPs, usually from latest dbSNP distribution.

Outputs

Name Type Description
errors TextFile File containing founds errors.

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.

Test cases

Test case Parameters IN
reference
IN
variants
IN
dbsnp
OUT
errors
case1 properties reference variants dbsnp (missing)

memory=1g


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