Idat file processing issue with command line cli

Question

[1769mkc]

The illumina tool which I used this and the file I used for canine is this file

     array-analysis-cli/./array-analysis-cli.exe genotype call --bpm-manifest CanineHTS-24_20095584_B1.bpm --cluster-file CanineHTS-24_20095584_B1_ClusterFile.egt --idat-folder 208849480027/ --output-folder gtc/
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:26 6591]: Starting Processing...
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:26 6744]: Inputs:
Manifest file (.bpm): D:\NRD_DATA\Canine_208849480027\CanineHTS-24_20095584_B1.bpm
Cluster file: D:\NRD_DATA\Canine_208849480027\CanineHTS-24_20095584_B1_ClusterFile.egt
IDAT input: D:\NRD_DATA\Canine_208849480027\208849480027\
GenCall score cutoff: 0.15
Output folder: D:\NRD_DATA\Canine_208849480027\gtc\
Number of threads: 1
info: ArrayAnalysis.Services.SampleFactory[0]
      [01:22:26 6750]: Crawling D:\NRD_DATA\Canine_208849480027\208849480027\...
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:26 6825]: Number of samples: 24
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:26 6829]: Loading D:\NRD_DATA\Canine_208849480027\CanineHTS-24_20095584_B1.bpm...
info: ArrayAnalysis.Services.SampleNormToGenCallSvc[0]
      [01:22:27 9377]: Loading D:\NRD_DATA\Canine_208849480027\CanineHTS-24_20095584_B1_ClusterFile.egt...
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:28 8266]: Genotyping samples...
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:28 8300]: Normalizing 208849480027_R01C01...
info: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:29 7436]: Gencalling 208849480027_R01C01...
warn: ArrayAnalysis.Services.GenCallingService[0]
      [01:22:29 8068]: Failed to normalize and gencall sample: 208849480027_R01C01, it will be skipped. Error: The given key 'BICF2G63010014' was not present in the dictionary.

This fails, when I do the run in array-analysis-cli it fails but when I do the same with genomestudio it works I can get the plink output.

The naming patter of my files are like this small example

    208849480027/*.idat
208849480027/208849480027_R01C01_Grn.idat  208849480027/208849480027_R05C01_Grn.idat  208849480027/208849480027_R09C01_Grn.idat
208849480027/208849480027_R01C01_Red.idat  208849480027/208849480027_R05C01_Red.idat  208849480027/208849480027_R09C01_Red.idat

I would like to know what issue is with the CLI that is triggering the issues.

[Giulio Genovese]

You are getting error:

Error: The given key 'BICF2G63010014' was not present in the dictionary.

Indeed, variant BICF2G63010014 is present in the .bpm file but not in the .egt file. This is odd and likely an issue with the Illumina manifest files.

The CanineHTS-24_20095584_B1.bpm includes 172032 probes while the CanineHTS-24_20095584_B1_ClusterFile.egt includes 169498 probes. It seems as if Illumina updated the .egt file by removing some probes but did not similarly update the .bpm file causing a discrepancy.

I could update the free BCFtools/idat2gtc tool to process IDAT files despite this discrepancy if you are interested.

[1769mkc]

I could update the free BCFtools/idat2gtc tool to process IDAT files despite this discrepancy if you are interested.

that would be really helpful

The other doubt is how genomestudio is not getting this error ? Is it because of this "It seems as if Illumina updated the .egt file by removing some probes but did not similarly update the .bpm file causing a discrepancy."

[GenoMax]

Is it because of this "It seems as if Illumina updated the .egt file by removing some probes but did not similarly update the .bpm file causing a discrepancy."

Email Illumina tech support to ask.

[Giulio Genovese]

Can you email a pair of IDAT files causing this issue to the author of BCFtools/idat2gtc so that the error can be reproduced?

[1769mkc]

yes i can share a pair of the idat files, I have sent to the email address