Split One Bam File Into Multiple Ones (One Per Feature From A Gff File)

Question

[Nicolas Rosewick]

Hi,

I've a bam file and a gff file containing features (like coordinates of ncRNA). Is it possible to split this bam file into multiple bam files to have one bam file per feature (And maybe specify parameters like -f in intersectBed )

Thanks a lot,

N.

Answer 1

[Pierre Lindenbaum]

loop over the features of your gff and use samtools view to save each bam.

Usage:   samtools view [options] in.bam region

Options: -b       output BAM
         -o FILE  output file name [stdout]