Partitioning or slicing up a BAM file

[nimrod337]

Okay, I cannot for the life of me find any results on this site, or the internet as a whole about cutting up a BAM file to make a smaller BAM file.

I want to send a chunk of my BAM file off to a developer because the program I am trying to use is giving me some errors. But he cannot recreate the error without my BAM file. Of course BAM files are huge, so I cannot just email him the whole thing, so I was hoping I could just cut it up, and maybe host a chunk of it on my Dropbox for him to download.

Anyone have a clue as to how to do this? It doesn't need to be partitioned in a specific way, just reduced in size. I feel like there must be a simple solution out there, but I am in no way an expert, and my google-fu is lacking.

Thanks
A

[GenoMax]

http://www.1000genomes.org/faq/how-d...ction-bam-file Change the chromosome range to suite your needs.

[kmcarr]

You can randomly subsample a BAM file with samtools (the view sub-command specifically). I believe this function was added in a later version of samtools but not sure exactly which release; I'm using version 0.1.19-44428cd.

Usage:   samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b       output BAM
         -h       print header for the SAM output
         -H       print header only (no alignments)
         -S       input is SAM
         -u       uncompressed BAM output (force -b)
         -1       fast compression (force -b)
         -x       output FLAG in HEX (samtools-C specific)
         -X       output FLAG in string (samtools-C specific)
         -c       print only the count of matching records
         -B       collapse the backward CIGAR operation
         -@ INT   number of BAM compression threads [0]
         -L FILE  output alignments overlapping the input BED FILE [null]
         -t FILE  list of reference names and lengths (force -S) [null]
         -T FILE  reference sequence file (force -S) [null]
         -o FILE  output file name [stdout]
         -R FILE  list of read groups to be outputted [null]
         -f INT   required flag, 0 for unset [0]
         -F INT   filtering flag, 0 for unset [0]
         -q INT   minimum mapping quality [0]
         -l STR   only output reads in library STR [null]
         -r STR   only output reads in read group STR [null]
         [COLOR="Red"]-s FLOAT fraction of templates to subsample; integer part as seed [-1][/COLOR]
         -?       longer help

For example the following command will create file named subSample.bam with a random 1% sample taken from Sample.bam

samtools view -b -o subSample.bam -s 0.01 Sample.bam

[dpryan]

Just to add to what the others have mentioned, ensure that the subsampled BAM file reproduces the problem. It's never very fun to try and diagnose a problem when you receive a BAM file that can't reproduce it P

[nimrod337]

Wow, awesome. Thanks you guys.
This site has really saved my A$$.

Thanks again.