Convert annotated vcfs to maf

[FriederikeHanssen]

This is the script I use to convert the annotated vcf.gz to maf:

for file in $(ls *.vcf.gz | grep -v renamed | grep -v merge); do
     echo $file
     my_array=($(echo $file | tr "_" "\n"))

     echo "${my_array[3]}"
     echo "${my_array[1]}"

     bgzip -d $file

     bcftools view -f PASS ${file/.vcf.gz/.vcf} > ${file/.vcf.gz/_PASS.vcf}

     vcf2maf.pl --input-vcf  ${file/.vcf.gz/_PASS.vcf} --output-maf ${file/.vcf.gz/.maf} --tumor-id "${my_array[1]}" --normal-id "${my_array[3]}" --ref-fasta /nfsmounts/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta  --ncbi-build GRCh38 --inhibit-vep --vcf-tumor-id TUMOR --vcf-normal-id NORMAL
done

conda environment needs vcf2maf & bcftools & pbgzip. The renaming of the samples with the qbic barcodes is important for the downstream analysis. The array line works for the Strelka files, it would possibly need to be adapted if the vcf files have other naming conventions, as with Manta I think (or in case the naming gets changed in a future sarek release)