Code for alignment and BAM reprocessing

calculate all md5 checksums in input folder and subfolders

    snakemake -s md5sum_files.smk --profile=cubi-dev -j1

run alignment for FASTQ files in input folder and subfolders

    sbatch run_alignment_v2.sh

merge all the lane bam files into one sample bam file

    sbatch merge_bams.sh

deduplicate the merged bam files

    sbatch run_dedup_bams.sh

run bqsr for the deduplicated bam files

    sbatch run_bqsr_bams.sh