How to run apt-geno-qc with call rate and treshold?

Question

[anamaria]

Hello,

I am trying to run apt-probeset-genotype from: https://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-genotype.html

My data is: Affy500K

They say there that: " For Mapping 500K data the recommended per-chip spec is a call rate of 93% using DM at a threshold of 0.33"

Does that mean that prior running apt-probeset-genotype I have to run apt-geno-qc https://www.affymetrix.com/support/developer/powertools/changelog/apt-geno-qc.html

and if yes how I would specify this 93% call rate and 0.33 threshold?

Would this require running:

apt-geno-qc \
    --cdf-file  GenomeWideSNP_6.cdf \
    --qcc-file  GenomeWideSNP_6.qcc \
    --qca-file  GenomeWideSNP_6.qca \
    --cel-files cel.txt \
    --out-file  qc.txt

and setting in GenomeWideSNP_6.qca file em.cutoff=0.93?

https://www.affymetrix.com/support/developer/powertools/changelog/apt-geno-qc.html

Thanks Ana