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DepthOfCoverage for whole genome: skipped few regions

NeelamNeelam BlacksburgMember

I used following command to get coverage data for entire genome:
java -Xmx2g -jar ~/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T DepthOfCoverage -R ~/Gmax_189.fa -o DoCov_dedup -I dedup.bam.list

Coverage was not reported for 36025109 bases. Many skipped bases fall one after another in the genome to form big continuous regions. I do not understand, why these regions were skipped. Usually if there was no mapping, the coverage value should be reported as 0.

Appreciate some insight into this issue! Thank you.

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  • NeelamNeelam BlacksburgMember

    Thank you. Those are all strings of ambiguous bases. What will be the situation for single ambiguous base in middle of canonical bases?

  • NeelamNeelam BlacksburgMember

    I found DepthOfCoverage is reporting for ambiguous bases in coverage output file.
    Attached are the snapshots of: (1) coverage output for small region on chromosome 1;
    image

    and (2) alignments output in this region.
    image

    Position #21956 is starting of ambiguous region that is more than 8K long in reference genome.
    How can I get rid of these points from depth output file, without actually eliminating the regions of no mapping?

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