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Published 20 hours ago • verified publisher icon pughlab

'chr' confusion

Open dharbi opened this issue 8 years ago • 2 comments

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).

dharbi avatar Sep 30 '16 16:09 dharbi

I observed this too. I added some modification in the VisCap.R to fix it, no need for an external command.

biocyberman avatar Oct 06 '16 07:10 biocyberman

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

leefall avatar Dec 13 '19 07:12 leefall