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DepthOfCoverage for whole genome: skipped few regions

NeelamNeelam BlacksburgPosts: 6Member

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.


Best Answers


  • NeelamNeelam BlacksburgPosts: 6Member

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

  • NeelamNeelam BlacksburgPosts: 6Member

    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;

    and (2) alignments output in this region.

    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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