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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Generating signal intensity for axiom arrays #100

Open sophie-03 opened 1 year ago

sophie-03 commented 1 year ago

Hello,

I am trying to generate signal intensity data from raw CEL files. My data is from the UK Biobank Axiom arrays by Affymetrix. I am presuming the correct instructions to follow are those specific to the Axiom array provided by Professor Kirov. in these instructions, the Axiom_UKB_WCSG.xml file is used. Where can I obtain this file?

Also, issue #46 indicates that it is fine to use the affygw6 hmm file for PennCNV using the UKB axiom array data. In this case, is it also ok to use the genome-wide 6.0 array instructions to generate the signal intensity data, or should only the Axiom instructions from Professor Kirov be used?

Thanks in advance.

shadrinams commented 7 months ago

Just talked to the Affymetrix team about the first step in the Kirov's pipeline. Here is their suggestion/update:

"Try running apt-genotype-axiom with the r5 library files. You should get the output you need, as apt-probeset-genotype has been replaced by apt-genotype-axiom in the current version of APT.

The command would be:

apt-genotype-axiom \ --analysis-files-path \ --arg-file /Axiom_UKB_WCSG_SNPSpecificPriors_Step2.r5.apt-genotype-axiom.AxiomGT1.apt2.xml \ --cel-files /genotyping_cel_files.txt \ --out-dir <output directory/ \ --analysis-name \ --log-file <output directory/Logs/ProbeSetSummarisationAnalysis.txt "

You can find Axiom_UKB_WCSG_SNPSpecificPriors_Step2.r5.apt-genotype-axiom.AxiomGT1.apt2.xml file within the library files on the official page of your Affy chip.