search

freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
143 stars 24 forks source link

how to convert CEL to CHP? #43

Closed lizhan96 closed 1 year ago

lizhan96 commented 2 years ago

After I install bcftools, I follow the README document and run the following code, but there is a error message. path_to_output_folder="..." cel_list_file="..." apt-probeset-genotype \ --analysis-files-path . \ --xml-file GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml \ --out-dir $path_to_output_folder \ --cel-files $cel_list_file \ --special-snps GenomeWideSNP_6.specialSNPs \ --chip-type GenomeWideEx_6 \ --chip-type GenomeWideSNP_6 \ --table-output false \ --cc-chp-output \ --write-models \ --read-models-brlmmp GenomeWideSNP_6.generic_prior.txt

The question is that what software should be install when use [apt-probeset-genotype]?

freeseek commented 2 years ago

Well, I am not the writer of the Affymetrix tool apt-probeset-genotype. What error message are you getting?

freeseek commented 2 years ago

If the error is: FATAL ERROR:Can't read header for GenomeWideSNP_6.cdf. Description: Unable to open the file.

Then you need the file GenomeWideSNP_6.cdf in the analysis files path. You can follow the instruction here to obtain that file