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  • how to calculate base-by-base coverage?

    for whole exom data (bam files), I want to calculate depth of coverage for given regions (supplied as bed file).
    furthermore, I also want to exclude bases with quality scores less that 30.

    can someone give me some hint on which software/pipeline to do this?
    thanks a lot

  • #2
    coverageBed from BEDTools would give you what you need in terms of coverage (http://bedtools.readthedocs.org/en/l.../coverage.html).

    Comment


    • #3
      Hi shuoguo;
      I can tell you two options.

      1)
      Code:
      bamtools coverage -in infile.bam -out output.txt
      2) Convert BAM file to BED first:

      Code:
      bedtools bamtobed -i input.bam > output.bed
      Then,
      Code:
      bedtools genomecov -d -i input.bed -g genomefile.txt
      Code:
      -d option prints coverage per base.
      The genome file should tab delimited and structured as follows:
      <chromName><TAB><chromSize>

      For example, Human (hg19):
      chr1 249250621
      chr2 243199373
      ...
      chr18_gl000207_random 4262

      Remember if you are analyzing human genome, you will be writing 3*10^9 lines in a text file if you want to report base by base. You may want to try with a smaller dataset first to see if you are getting what you want to get.

      Hope this helps.

      Comment


      • #4
        Sorry, I just realized you asked for a given region, not whole genome. I think you can do following using bedtools.

        Code:
        bedtools coverage -d -abam file.bam -b regions.bed

        Comment


        • #5
          Thank you rnaeye and GenoMax
          I also need to EXCLUDE bases that lave GQ less than 30. i am not sure if bed tools can do it?

          Comment

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