prep_files.sh

python3 ./wes.py WES \
    -i /mnt/gs21/scratch/mansourt/wes_gatk/raw_data \
    -o /mnt/gs21/scratch/mansourt/wes_gatk/output \
    --reference-fasta /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens_assembly38.fasta \
    --bed-file /mnt/gs21/scratch/mansourt/wes_gatk/exome_bed/sureSelect_V6_60M.bed \
    --gff-file /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens.GRCh38.109.gff3.gz \
    --nirvana-path /mnt/home/mansourt/annDB/Nirvana \
    --annovar-path /mnt/home/mansourt/annDB/annovar_source/annovar \
    --known-variants-snps /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens_assembly38.dbsnp138.vcf \
    --known-variants-indels /mnt/home/mansourt/annDB/broad_hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
    --known-variants-indels2 /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens_assembly38.known_indels.vcf.gz \
    --reference-index /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens_assembly38.fasta \
    --svd-prefix /mnt/home/mansourt/annDB/broad_hg38/Homo_sapiens_assembly38.contam \
    --generate-confs-only \
    --threads 12