How to craete snps map file?

1

Entering edit mode

7.5 years ago

forever ▴ 80

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 • 1.7k views

ADD COMMENT • link updated 7.5 years ago by GenoMax 141k • written 7.5 years ago by forever ▴ 80

1

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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 REPLY • link 7.4 years ago by WouterDeCoster 47k

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