smaller bam file given a bed file

[adrian]

Hi:

When I load accepted_hits.bam from Tophat and Junctions.bed into IGV to visualize splicing events for two samples, due to memory IGV responds slow.


I wanted to make a smaller BAM file from larger BAM file by supplying only those regions I see splicing differences (output from Cuffdiff).

Given a GTF or BED file and large size accepted_hits.bam BAM file, can I make smaller size BAM file.

For a given position, I know how to do;
samtools view bam chr1:11111-22222...

I don't know how I can supply BED or GTF to samools..

Thanks
Adrian

[dariober]

I don't know how I can supply BED or GTF to samools..

Hi- Check the -L option in samtools view.
Dario

samtools view -h

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
         -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]
         -s FLOAT fraction of templates to subsample; integer part as seed [-1]
         -?       longer help

[adrian]

Oh.. I missed it. That was embarrassing.. it was right there.

Thanks for pointing out.

-Adrian.