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splitbam splits a BAM by chromosomes.
Using the reference sequence dictionary (*.dict
), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.
java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)
__CHROM__
and end with .bam