bamCleaner

Overview

Cleans up BAM files by fixing MAPQ issues in unmapped reads and automatically validates BAM file integrity.

bamCleaner.sh

sbatch --job-name=[jobName] ~/atelier/bin/bamCleaner.sh -i [input] [options]

Option	Description
`-i [input]`	Input BAM file or file list (one path per line)
`-o [outputDir]`	Output directory for cleaned BAMs (default: same as input)
`-p [prefix]`	Output filename prefix (default: original_name.cleaned)
`-t [threads]`	Number of threads to use (default: auto-detect)
`-r`	Remove unmapped reads entirely (default: keep with MAPQ=0)
`-n`	Dry run
`-h`	Display help message

Clean a single BAM (automatic validation always happens)

sbatch --job-name=clean-bam ~/atelier/bin/bamCleaner.sh \
    -i sample.bam

Remove unmapped reads with automatic validation

sbatch --job-name=clean-remove ~/atelier/bin/bamCleaner.sh \
    -i sample.bam \
    -r

Batch processing with automatic validation

sbatch --job-name=clean-batch ~/atelier/bin/bamCleaner.sh \
    -i bam_list.txt

Dry run (shows what would happen, including validation)

sbatch --job-name=clean-preview ~/atelier/bin/bamCleaner.sh \
    -i sample.bam \
    -n