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Variant calling in RNAseq data using HaplotypeCaller and VariantFiltration in GATK. The function with default values follows the GATK best practices as seen on 12.09.2016

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


Name Type Mandatory Description
reference FASTA Mandatory The reference fasta file.
in BAM Mandatory Input BAM file.


Name Type Description
out VCF Filtered Variant calls


Name Type Default Description
callEmit string "20.0,20.0" Comma-separated values of stand_call_conf and stand_emit_conf parameters respectively.
cluster string "3" Minimum number of variants in a defined window to consider them clustered.
filterNames string "FS,QD" Comma-separated names of filters to be applied. For example use "FS,QD" for two filters.
filteringOptions string "" Other options to be passed to VariantFiltration.
filters string "FS > 30.0,QD < 2.0" Comma-separated filters to be applied. The length and order should match the one in filterNames.
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.
haplotypeOptions string "" Other options to pass to HaplotypeCaller
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.
window string "35" Window size in bp for clustered variants filtering. Set to 0 to deactivate.

Test cases

Test case Parameters IN
case1 properties reference in (missing)


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