Is there any repositories where I can find a vcf file for dbSNP release 131?

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Debasish Mukherjee

I found this onlie..Let me me know if it dose not work..

http://statsandgenomes.wordpress.com/2011/11/06/a-python-script-to-make-a-dbsnp-vcf-file/

http://ngsda.blogspot.in/2011/07/mouse-dbsnp-vcf.html

Lucie Hutchins

VCF in NCBI are stored by organism - check ftp://ftp.ncbi.nih.gov/snp/organisms/

then click on your organism of interest to access its vcf file.

Human vcf - ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/

Mouse vcf - ftp://ftp.ncbi.nih.gov/snp/organisms/mouse_10090/

Sourav Nayak

Thanks Debasish and Lucie.

@ Debasish: Codes are not validated. I will try anyways.

@ Lucie: The links you have posted is for current release but not dbSNP131, what I am looking for.

Mohamed Ashick

I dont have the dbSNP file with me to check, but if my memory is good I think you will have a tag mentioned in the VCF file which says from which version the SNP was added. Like for each SNP you will have dbsnp129, dbsnp132, etc... You can just pick whichever is less than or equal to dbsnp131. Correct me if am wrong.

@Ashick

I also thought about this. But when I greped with the tag, the count came too small. Just for an idea I am giving a approx count. According to dbSNP131 there are almost 30 million variants. Where in dbSNP137 release here are about 52 million variants in which 2 million variants containing dbSNP131 tag. Hope you will get the idea. Thanks a lot.

Sorry for being late to respond. I have tried that also. But in vain. Obviously the number of variants increased almost 10 times, but still there are ~10 millions missing counts. That is also quite obvious, because there will be so many dbSNP131 entries which must have been got updated due to incorporation of new segments into human genome. So I guess it is not enough to serve the purpose. Correct me if I am wrong.