I am trying to get base coverage information, and am using the --PER_BASE_COVERAGE output from Picard tools to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such:

12      12258595        12258695        +       TARGET1
12      12258696        12258795        +       TARGET2
12      12258796        12259791        +       TARGET3

However, when I look at my covg file, I see the following:

chr    pos    target   covg 
12  12258595        TARGET1|TARGET2|TARGET3 510

Why would HSmetrics group these targets together, and how can I separate them?

  • $\begingroup$ Question is also asked on biostars. $\endgroup$ – finswimmer Feb 25 '19 at 7:43
  • $\begingroup$ Hello @Blaze9, I don't understand your question. Would you maybe explain bit what are the targets? Are they read groups? (disclaimer, I am not a Picard tools user); I usually use samtools for this. $\endgroup$ – Kamil S Jaron Feb 25 '19 at 9:34
  • $\begingroup$ Hi @KamilSJaron, the targets are either tiling regions or exons/introns. I can checkout samtools to see if it provides better results. The per_target_coverage output does not combine the targets which is the weird part. Thanks! $\endgroup$ – Blaze9 Feb 25 '19 at 16:14
  • 1
    $\begingroup$ Ah, I see. Maybe you want to edit your question and add as many details as you can (such those you wrote in the comment) :-). $\endgroup$ – Kamil S Jaron Feb 25 '19 at 17:42

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