generate_affy_geno_cluster.pl no SNP or CN markers

[sophie-03]

Hello Dr Wang,

I am trying to generate a canonical genotype clustering file using generate_affy_geno_cluster.pl. However, my output file is empty due to "0 SNP marker and 0 CN markers being analysed", despite my locfile containing 12968 markers (chr22 only).

I am using the UK Biobank Axiom array and have been following the instructions by Professor Kirov. I have successfully completed the apt-probeset-genotype step, and have generated a call, confidence, summary and report file.

This is my command line input:

~/bin/gw6/bin/generate_affy_geno_cluster.pl AxiomGT1.calls.txt AxiomGT1.confidences.txt AxiomGT1.summary.txt --nopo
wer2 -locfile ../chr22_loc.txt -sexfile ../batch2_sexfile.txt -out batch2.genocluster

And this is these are the notices I get:

NOTICE: The --confidence_threshold argument is automatically set as 0.01 (default for Affymetrix Power Tools calling)
NOTICE: Reading marker-location-file ../chr22_loc.txt ... Done with 12968 markers!
NOTICE: A total of  390 males and 513 females are found in the signal file AxiomGT1.summary.txt
WARNING: A total of 830114 markers do not have chromosome annotation in locfile ../chr22_loc.txt and were skipped
NOTICE: A total of 0 SNP markers have been analyzed to construct canonical clustering positions
NOTICE: A total of 0 CN markers have been analyzed to construct canonical clustering positions

The output file, batch2.genocluster, is empty.

Do you know why this is? Many thanks.