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AnnTools

Runs one of the AnnTools variant annotator suite's scripts. Verify that anntoolsPath points to an AnnTools installation location. The MySQL server settings are read from the config.txt file in the AnnTools installation directory, so the user need not care about them once anntools has been deployed. The publication is available from AnnTools: A Comprehensive and Versatile Annotation Toolkit for Genomic Variants

Version 0.1
Bundle sequencing
Categories External
Authors Lauri Lyly (lauri.lyly@helsinki.fi)
Issue tracker View/Report issues
Requires bash
Source files component.xml main.bash
Usage Example with default values

Inputs

Name Type Mandatory Description
variants TextFile Mandatory Variants in VCF or pileup format

Outputs

Name Type Description
array Array<VCF> Output VCF files.
log BinaryFolder All other files.

Parameters

Name Type Default Description
anntoolsPath string "/opt/anntools" AnnTools installation path which needs to contain either run_cnv.sh, run_indel.sh or run_snp.sh, depending on the annotation mode. The standard installation has them.
format string "pileup" Either pileup or vcf. Match your input file type. CNV may only accept VCF files.
mode string "snp" One of snp, indel or cnv. CNV only accepts VCF files, otherwise you can choose.

Test cases

Test case Parameters IN
variants
OUT
array
OUT
log
case_cnv properties variants array log

format=vcf,
mode=cnv,
anntoolsPath=/opt/anntools,
metadata.timeout=0,

case_indel properties variants array log

format=vcf,
mode=indel,
anntoolsPath=/opt/anntools,
metadata.timeout=0,

case_snp properties variants array log

format=pileup,
mode=snp,
anntoolsPath=/opt/anntools,
metadata.timeout=0,


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