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'chr' confusion #5

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dharbi opened this issue Sep 30, 2016 · 2 comments
Open

'chr' confusion #5

dharbi opened this issue Sep 30, 2016 · 2 comments

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@dharbi
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dharbi commented Sep 30, 2016

I have noticed getting always normal results with mislabeled plots when 'chr' word is within the interval list file provided, or in GATK DepthOfCoverage output files (*sample_interval_summary).
Please be sure that these files are without 'chr' word (i.e., chr14 should be modified to 14, using for example sed command).
@biocyberman
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I observed this too. I added some modification in the VisCap.R to fix it, no need for an external command.

@leefall
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leefall commented Dec 13, 2019

I did pull request of the script for both "chr"prefix chromosome and only chromosome number.

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@biocyberman @leefall @dharbi