Converting Illumina Omni 1 Quad v1.0 to hg19
I have data from a Illumina Omni Quad 1 v1.0 array and need to convert this to hg19/GRCh37.
The easiest way I know of is to use the strand files from here: http://www.well.ox.ac.uk/~wrayner/strand/sourceStrand/index.html
However, the file has already been preprocessed so the cnv IDs that are required by the strand file have been replace with rsIDs in my data. The positions do not match either: the strand file's positions are hg19 but my data has positions from the chip.
How can I align my data to hg19? Is there away to get the cnv IDs from the positions in my data and then use the strand file to convert to hg19?
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For reference, a SNP with rsID such as rs13303227 has position 882608 in my file but has position 892745 in hg19.
Could that be hg18?
I believe it's position 882858 on hg18. Still not quite right. If you look it up on dbsnp (https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=13303227), there are some sources in the records section that have the position I specified. Do you happen to know what these are?
rs13303227 is at chr1:882608 in hg18/dbSNP build 130
I checked this using the UCSC genome browser.
You can use Liftover to convert between genome builds.
manuscript here worked with same platform and reported same SNV (rsID) with matching position from OP. Build they have used in their studies is b36.