Mercurial > repos > elixir-it > mutect2

comparison mutect2.xml @ 9:a517190d2b3d draft

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Uploaded
author elixir-it
date Sat, 21 Sep 2019 13:21:54 -0400
parents 467fcccde14d
children e3662508ee26
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8:467fcccde14d 9:a517190d2b3d
36 ln -s $alleles alleles.vcf 36 ln -s $alleles alleles.vcf
37 #end if 37 #end if
38 38
39 ##TODO creation of .dict file of the genome required by mutect2 to run 39 ##TODO creation of .dict file of the genome required by mutect2 to run
40 #if $reference_source.reference_source_selector == "history" 40 #if $reference_source.reference_source_selector == "history"
41 java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log && 41 java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
42 #end if 42 #end if
43 43
44 ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it 44 ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
45 ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned 45 ##and move the .jar file to \$CONDA_PREFIX/opt/gatk-3.8/ then the mutect2 command is runned
46 gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ; 46 gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ;
47 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 47 java -jar \$CONDA_PREFIX/opt/gatk-3.8/GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output
48 #if $reference_source.reference_source_selector == "history" 48 #if $reference_source.reference_source_selector == "history"
49 -R genome.fa 49 -R genome.fa
50 #end if 50 #end if
51 #if $reference_source.reference_source_selector == "cached" 51 #if $reference_source.reference_source_selector == "cached"
52 -R $reference_source.ref_file.fields.path 52 -R $reference_source.ref_file.fields.path