Convert TCGA MAFs to VCFs to use to annotate other VCF files with variant frequency in the various TCGA projects (including pancan12).

tcga-maf-to-vcf.sh

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 

if [ ! -f maf2vcf.pl ]; then
  wget https://raw.githubusercontent.com/ckandoth/vcf2maf/master/maf2vcf.pl
fi

if [ ! -f vcfsorter.pl ]; then
  wget https://gist.github.com/dakl/b14aa4648a1ef17cee8c/raw/f1de9791460a3a1f60217cd2e6c0cd72ae78ae91/vcfsorter.pl
fi

#MAF=/home/daniel.klevebring/Crisp/dakl/tcga-maf-to-vcf/somatic_mafs_cleaned/thca_cleaned.maf
MAFS=(`find $WORKDIR/somatic_mafs_cleaned|grep maf$`)
for MAF in ${MAFS[@]}; do
  TMP=`basename $MAF`
  GRP=tcga-${TMP/_cleaned.maf/}
  echo -n "$GRP"
  mkdir -p $GRP

  perl maf2vcf.pl --input-maf $MAF --output-dir $GRP --ref-fasta $REF
  VCFS=(`find $GRP|grep vcf$`)
  
  #VCF=laml/TCGA-AB-2802-03B-01W-0728-08_vs_TCGA-AB-2802-11B-01W-0728-08.vcf
  # sort the generated VCFs
  for VCF in ${VCFS[@]}; do
    SORTEDVCF=${VCF/.vcf/_sorted.vcf}
    perl vcfsorter.pl $DICT $VCF |vt normalize -r $REF - |bgzip > $SORTEDVCF
    tabix -p vcf $SORTEDVCF 
    #rm $VCF
  done

  SORTEDVCFS=(`find $GRP|grep _sorted.vcf$`)
  FINALVCF=${GRP}-somatic.vcf.gz
  bcftools merge --merge none --force-samples ${SORTEDVCFS[@]} |bgzip > $FINALVCF
  tabix -p vcf $FINALVCF
  
  echo " done."
  
  rm -r $GRP
done