CNVR output file contents

[Melody Rynerson Palmer]

Hello,

Is there a simple reason why there would be no entries in the {prefix}_PlinkP_CNVR_ALL_ReviewdCNVRs.txt file, but a few hundred in the {prefix}_PlinkP_CNVR_ALL_ReviewdCNVRs_verbose.txt file? There are also entries in the _ControlEnriched.txt files, just not the main ones. 

Also I'm having trouble importing the verbose file into R or Excel accurately. Many of the columns are empty, so it's not assigning them to the correct header regardless of whether I tell it it's tab or space delimited, and sometimes it's hard to figure out which values match which column names. Any tips for that?

My final problem is that the UCSC custom track files are getting rejected with the following error: Error Unrecognized binary data format in file {prefix}_PlinkP_CNV_UCSC_bedfile_ForCustomTrackReview.txt

I'm still looking into this one but if anyone has suggestions or success I'd love to see an example.

Thank you!

Melody Palmer

mry...@uw.edu

[Joe Glessner]

Hello,

It sounds like a process control problem with the code. The code is exiting without the file being written fully. The verbose.txt file is the main one while the others are generated as the last step of InsertPlinkPvalues.pl. To the code attached, I added a close statement for each of the filehandles which should prevent the code from exiting without completing the file writing.

I added a looser error handling for unmet dependencies (.stats,ParseCNV.log,Plink.log) for InsertPlinkPvalues.pl which may have been a mistake because it results in blank fields which can be confusing. Check the .log file for “WARNING:” lines which will tell you what unmet dependencies exist and try copying those files into the working directory. The reports should be tab delimited, not space delimited.

Could you run these couple of tests on your UCSC track to help narrow down the problem?
awk '{print NF}' {prefix}_PlinkP_CNV_UCSC_bedfile_ForCustomTrackReview.txt | sort | uniq -c
awk '{print $1}' {prefix}_PlinkP_CNV_UCSC_bedfile_ForCustomTrackReview.txt | sort | uniq -c

Joe Glessner

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