Sentrix Array Genotyping

Question

[joo]

Hi all,

I am currently trying to figure out how to work with genotyping data generated by a Sentrix array. The data I have is an output file from the Illumina GenomeStudio Software, namely a SampleName_FinalReport.txt file which contains the columns

Sample ID , Sample Name, SNP Name, Chr, Position, Allele1 - Forward ,Allele2 - Forward, B Allele Freq, Log R Ratio, GC Score

The genomic positions however don't seem to match any common reference genome. For example, there is a SNP named 1:110228505_CNV_GSTM1, indicating that chromosome 1, position 110228505 should lie in the GSTM1 gene, however this is not the case for hg16 to 19 and hg38. I want to compare these data with other data generated in a different way. Now my question is: How do I find out how to associate these genomic positions with a more common reference genome such as hg38?

[Pierre Lindenbaum]

"1:110228505_CNV_GSTM1" it's labelled as CNV. Do you know the end position for this CNV ?

[joo]

For each of the samples there are 140 consecutive lines that have been labelled chr:position_CNV_GSTM1, the first one being 1:110228436_CNV_GSTM1 and the last one 1:110253065_CNV_GSTM1. Some of the SNPs in between are names like this: 1:110237876_CNV_GSTM1_ilmndup1.