Question: How to craete snps map file?
1
gravatar for forever
2.8 years ago by
forever80
forever80 wrote:

Hi every one, I have a list of SNPs (one millions) for the below format:

SNPs name   
rs7552632

chr1:109457160

rs7552714

rs7552841

rs7553178

I need to create SNPs.map file with the below format:

SNPs name   Chr     position

Rs678678     1         1561131345

I download from dbSNPS all the SNPS location.

I need to get one line from snps list and search the reference file and retrieve the snps chr and its position. Is there is any R package or script to do it?

Some snps name written in chr#: position, so I need to separate the chromosome number from its position.

I appreciate any help.

snp • 728 views
ADD COMMENTlink modified 2.8 years ago by genomax70k • written 2.8 years ago by forever80
1

I see you have a lot of questions which could be solved be a quite basic script, so probably you should dive into a tutorial to learn basic R or python (or any other language).

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k
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