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Coverage summary #12

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dfornika opened this issue Sep 19, 2023 · 4 comments
Closed

Coverage summary #12

dfornika opened this issue Sep 19, 2023 · 4 comments

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@dfornika
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Generate a depth-of-coverage summary for each isolate, including:

  • Configurable depth threshold
  • Percent of genome that are below the depth threshold
  • .bed file showing low-coverage regions

...and possibly also

  • A .pdf plot of depth of coverage across the genome
@dfornika
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It would probably make sense to tie the depth threshold to our existing min_depth parameter:

tbprofiler-nf/nextflow.config

Line 21 in f871752

min_depth = 10

@dfornika
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A couple of tools that might be useful:

https://github.com/brentp/mosdepth

https://telatin.github.io/bamtocov

@taranewman
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This tool looks like it can produce a .bed file showing only low-coverage regions: https://github.com/telatin/covtobed

@dfornika dfornika mentioned this issue Sep 21, 2023
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@taranewman taranewman mentioned this issue Sep 23, 2023
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@dfornika
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Fixed by #13 and #14

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@dfornika @taranewman