Short pipeline that abstract unmapped reads from a bam file and convert to fastq files (PE reads)
python 2.7
SJM (simple job manager)
samtools
picard
bedtools
LSF batch system (or other)
To creat job file for GATK recalibrated bam:
run_unmap.py --bam NA12878.bam -r --out NA12878_test --tmp unmap_test -j na12878.sjm
To creat job file for regular bam:
run_unmap.py --bam NA12878.bam --out NA12878_test --tmp unmap_test -j na12878.sjm
To run job file : sjm na12878.sjm