SNP array liftover data with p values

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8.3 years ago

nuketbilgen ▴ 40

Hi,

We have canine snp array data (CanineSNPHD, ILLUMINA). The positions of the snps in this array are for Canine 2 genome version. So we need to convert this data to canine 3 gv. We used UCSC but it does not take the p values thus we need to delete row by row. It has been exhausting.

I hope that there is a tool for this conversion SNP positions with p values...

Also we saw that some of the snps in this array have changed chromosome for example

chr17 xyz SNP is on 12345 position in canine 2gv is now

chr18 ert SNP is on 78901 position in canine 3gv.

Could you help us? Please :(

liftover SNP p-value • 1.7k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.3 years ago by nuketbilgen ▴ 40

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It's unclear how the data you have looks like and why it's a problem to convert those to the newer genome build, please elaborate.

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k

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