How Can I Split Bam Into Chromosome (In A Loop) Using Samtools?

Question

[Hmm]

i want to split my bam file into chromosome and then index it.

Answer 1

[brentp]

Depending on your chromosomes, something like:

for chrom in `seq 1 22` X Y
do

    samtools view -bh $BAM chr${chrom} | samtools sort - chr${chrom}
    samtools index chr${chrom}.bam
done

[Hmm]

do we need to sort bam everytime we split it...or are we doing it to be on the safe side? Thanks for your response.

[brentp]

if your input bam is sorted, then you don't need to resort.

Answer 2

[Aaronquinlan]

bamtools has a "split" command for exactly this purpose.

[brentp]

Cool. I didn't know that. It's a bit sparse on docs

Answer 3

[Dan]

You can use this tool to do exactly that.

http://code.google.com/p/chrom-bed/