extract SNPs of certain gene
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5.4 years ago
marwa.cs91 ▴ 30

Hello all,I am new in plink analysis

I have Map file and I know that location (start /end) of CD2AP gene on chromosome 6 has base pairs 47,477,745 to 47,627,262

How can I use physical position column in MAP file to extract SNPs of this gene 

 

Any help will be appreciated

plink MAP gene SNPs location • 2.8k views
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5.4 years ago

Dear,

First you need to make sure which transcript you are interested. Keep in mind that the same SNP will have different cDNA coordinates between transcripts. Also you need to watch out for the genome version. Because g coordinates will also vary between different genome versions. Moving from your example, you can go to www.ensembl.org and write in the search CD2AP. You will see that the golden transcript is ENST00000359314 with 629 aminoacids. Now go to biomart at http://www.ensembl.org/biomart . Here select ensembl variation database, than select SNPs and Indels. Next from the left click on filters and go to gene associated filters. Here paste your gene ID which is ENSG00000198087. Next go to the attributes tab and select the coordinates you want (genomic, mRNA, coding sequence..etc) Download your results and you will have your SNPs.

I hope this helps,

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Thanks alot for your help I really appreciate

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1
Entering edit mode
5.4 years ago

plink cannot process isolated .map files; do you have an accompanying .ped? (If you don't, it might be simpler to write a short script for this job.)

If you do,

plink --file [.ped/.map filename prefix] --chr 6 --from-bp 47477745 --to-bp 47627262 --write-snplist --out [output filename prefix]

should give you the list you're looking for.

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Thanks alot for your help I really appreciate

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