Mercurial > repos > morinlab > vcf2maf

comparison vcf2maf.xml @ 9:4e76e1a1790e draft

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author morinlab
date Fri, 27 Jan 2017 20:10:26 -0500
parents 5ed8244ed6a7
children fa20a5e56cf2
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8:5ed8244ed6a7 9:4e76e1a1790e
7 echo \$ENSEMBL_VEP_84_INSTALL_DIR; 7 echo \$ENSEMBL_VEP_84_INSTALL_DIR;
8 ln -s $input_vcf ./input.vcf; 8 ln -s $input_vcf ./input.vcf;
9 perl \$VCF2MAF_SCRIPT_PATH/vcf2maf.pl 9 perl \$VCF2MAF_SCRIPT_PATH/vcf2maf.pl
10 --input-vcf ./input.vcf 10 --input-vcf ./input.vcf
11 --output-maf $output_maf 11 --output-maf $output_maf
12 12 --vep-forks 1
13 #if $sampleid_source.sampleid_selector == "bamfile": 13 #if $sampleid_source.sampleid_selector == "bamfile":
14 --tumor-id `basename $sampleid_source.sampleid_tumour | sed 's/.bam$//g'` 14 --tumor-id `basename $sampleid_source.sampleid_tumour | sed 's/.bam$//g'`
15 --normal-id `basename $sampleid_source.sampleid_normal | sed 's/.bam$//g'` 15 --normal-id `basename $sampleid_source.sampleid_normal | sed 's/.bam$//g'`
16 #else: 16 #else:
17 --tumor-id $sampleid_source.tumour_id 17 --tumor-id $sampleid_source.tumour_id