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

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,

bam split gff feature

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updated 14.6 years ago by Pierre Lindenbaum

• written 14.6 years ago by Nicolas Rosewick

1 answer

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]

• 0 views • link

written 14.6 years ago by Pierre Lindenbaum

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