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  • Getting Reads from Bam file

    Hello every one.

    I have a bam file which is approx 50gb from hiseq paired end data. I aligned it using BWA and now i am intersted in getting reads at particular location. i.e. for examle in chromosome 1 from (100000 - 101000). I would like to make a subset out from bam file with the above range. How can i do that ?

    Thank you for your help!!

  • #2
    Personally, I'd use samtools view to extract the region of interest into another BAM file. If you then want the reads then you could use Picard's SamToFastq.

    Cheers,
    Ian

    Comment


    • #3
      How can i specify the parameters for samtools view for extracting reads in that region?

      I see the below options in samtools.

      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

      Comment


      • #4
        A region can be presented, for example, in the following format: ‘chr2’ (the whole chr2), ‘chr2:1000000’ (region starting from 1,000,000bp) or ‘chr2:1,000,000-2,000,000’ (region between 1,000,000 and 2,000,000bp including the end points). The coordinate is 1-based.

        example

        samtools view aln.sorted.bam chr2:20,100,000-20,200,000

        Comment


        • #5
          thank you.. it worked

          Comment

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