dakl
/ tcga-maf-to-vcf.sh
Last active
February 12, 2021 14:06
Convert TCGA MAFs to VCFs to use to annotate other VCF files with variant frequency in the various TCGA projects (including pancan12).
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| REF=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta | |
| DICT=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.dict | |
| GATKJAR=/home/daniel.klevebring/projects/tcga-maf-to-vcf/GenomeAnalysisTK.jar | |
| WORKDIR=$HOME/Crisp/dakl/tcga-maf-to-vcf | |
| mkdir -p $WORKDIR | |
| cd $WORKDIR | |
| #unpack maf to workdir | |
| tar xvfz ~/projects/tcga-maf-to-vcf/pancan_cleaned_mafs.tar.gz |
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