[clean_cnv.pl] Error: the index for SNPs (...) are not found from signalfile

[fullrobot]

Hi,

I keep getting this error when running the clean_cnv.pl script to merge large CNVs. Error: the index for SNPs (kgp21634490 and kgp12494942) are not found from signalfile

I double checked my signal file and found those SNPs do exist so I'm not quite sure how to interpret this warning.

Thanks!

[kaichop]

what are the command line? The PFB file is checked, not signal file, when using clean_cnv.pl

On Tue, Mar 3, 2020 at 3:01 PM Adam Gleason notifications@github.com wrote:

Hi,

I keep getting this error when running the clean_cnv.pl script to merge large CNVs. Error: the index for SNPs (kgp21634490 and kgp12494942) are not found from signalfile

I double checked my signal file and found those SNPs do exist so I'm not quite sure how to interpret this warning.

Thanks!

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[fullrobot]

It's a bit complex but I'm running detect_cnv four times to call cnvs from autosomes, Chr X, Chr Y and Chr XY (Chr Y and Chr XY pfb files have been hacked to list the chromosome as X). Then I'm combining the cnv outputs into one report that I want to run through the clean_cnv script

here's the command line perl clean_cnv.pl combineseg merged_report.rawcnv --signalfile Input.txt --output combined_merged_report.rawcnv

where merged_report.rawcnv is the concatenated output from all 4 callers Input.txt is my raw output from illumina GenomeStudio, it should contain all of the SNP markers from our current chip.

Those probes are listed in Input.txt