Mercurial > repos > elixir-it > mutect2
changeset 8:467fcccde14d draft
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 25 Oct 2018 04:44:53 -0400 |
| parents | 2ebf2cd4f18f |
| children | a517190d2b3d |
| files | .shed.yml mutect2.xml |
| diffstat | 2 files changed, 11 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Oct 25 04:44:53 2018 -0400 @@ -0,0 +1,10 @@ +categories: +- Variant Analysis +description: 'MuTect2:somatic SNP and indel caller' +homepage_url: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php +long_description: | +MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller. +name: MuTect2 +owner: elixir-it +remote_repository_url: https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper +type: unrestricted
--- a/mutect2.xml Tue Jul 03 04:46:13 2018 -0400 +++ b/mutect2.xml Thu Oct 25 04:44:53 2018 -0400 @@ -44,7 +44,7 @@ ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ; - java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output + java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output #if $reference_source.reference_source_selector == "history" -R genome.fa #end if