Merge VCFs from 19 TCGA projects to a pancan19 VCF

tcga-vcfs-to-pancan19.sh

#!/bin/bash

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
 

VCFSTOMERGE=(`find -maxdepth 1 |grep \/tcga-|grep vcf.gz$|grep -v pancan`)
cnt=${#VCFSTOMERGE[@]}
for ((i=0;i<cnt;i++)); do
  VCFSTOMERGE[i]="-V ${VCFSTOMERGE[i]}"
done

PANCAN19VCF=tcga-pancan19.vcf.gz
java -jar $GATKJAR -T CombineVariants -R $REF --genotypemergeoption UNIQUIFY ${VCFSTOMERGE[@]} -o $PANCAN19VCF