Idat file processing issue with command line cli
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.
0 answers
No answers yet.
Log in to answer this question.
You are getting error:
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.
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."
Email Illumina tech support to ask.
Can you email a pair of IDAT files causing this issue to the author of BCFtools/idat2gtc so that the error can be reproduced?
yes i can share a pair of the idat files, I have sent to the email address