Mercurial > repos > elixir-it > mutect2

comparison mutect2.xml @ 11:057bce4b4f93 draft default tip

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author elixir-it
date Wed, 02 Oct 2019 04:39:04 -0400
parents e3662508ee26
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10:e3662508ee26 11:057bce4b4f93
41 java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log && 41 java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
42 #end if 42 #end if
43 43
44 ##TODO gatk mv_untar_gatk take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it 44 ##TODO gatk mv_untar_gatk take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
45 ##and move .jar and command is runned 45 ##and move .jar and command is runned
46 sh $__tool_directory__/mv_untar_gatk.sh && 46 bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
47 47
48 java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output 48 java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output
49 #if $reference_source.reference_source_selector == "history" 49 #if $reference_source.reference_source_selector == "history"
50 -R genome.fa 50 -R genome.fa
51 #end if 51 #end if