Hi, I have been doing some analysis from SNP-chip data using HomozygosityMapper...to complement homozygsity analysis I have also done using Plink. The chip used (Illumina Infinium HumanCoreExome-24 chip) is not listed under the chip options at the 'upload genotypes' stage in HomozygosityMapper. I initially uploaded under the 'Illumina: any array not listed here' option and found results to be quite different to Plink (many false +ves; long runs of homozygosity that contained lots of heterozygous genotypes upon closer inspection).
I have uploaded under several different illumina chip options in HomozyosityMapper, and each seems to come up with very different results. Could anyone suggest the most suitable chip option for uploading data? These are the options given for Illumina chips...
Illumina HumanOmni1-Quad, IlluminaHumanOmni1S, Illumina HumanOmni2.5, Illumina HumanOmni2.5.1.8-v1.1, Illumina HumanExpressExome-8v1, Illumina HumanExpressExome8v1.2, Illumina (any array not listed here).
Many thanks!
