How to convert Affymetrix Cytoscan HD to PLINK

Question

[Jorrit]

Hi all,

In short: I'm trying to get from my Affymetrix Cytoscan HD array data to PLINK format.

I have the genotyped array data (.cychp) and because I didn't find any tools to get from that to PLINK (except Affy2sv of which the wiki has dissapeared and I can't get in contact with the authors), I tried to convert the data myself.

As of now, I'm trying to annotate the genotype calls with rsIDs from dbSNP, but I'm getting a low hit rate, i.e. about 35%.

• I converted the cychp calls to a bed file, and tried annotating that bed file with dbSNP vcf.
• I also tried ANNOVAR and VEP (however, VEP needs a vcf and I'm unsure how to make that from cychp).
• Affy2vcf (bcftools plugin) might work to convert to vcf, but that would require cytoscan.annot.csv and I only have .db (so converting the db to csv might work for this)

Does someone have an idea that would get me either a step in the right direction, or directly to my destination?

Thanks in advance,

Jorrit