Dbsnp In Vcf Format

Question

[Andrea_Bio]

Hello

I have seen that dbSNP makes human SNP data available in VCF 4.0 format but not for other organisms. I would like to have bovine SNP data in VCF format for use with VCFTools.

Does anyone have any experience of converting dbSNP XML or ASN1 into VCF? Is there a resource available to do this? Or perhaps there is a tool to convert dbSNP into an intermediate format which would them be converted to VCF. I couldn't find anything along these lines but I wouldn't want to reinvent the wheel.

Or perhaps I am missing an alternative approach such as another variant file format which there exists the equivalent of VCFTools

Does anyone know if dbSNP have any plans to release data for other species in VCF format?

Thanks a lot

[Pierre Lindenbaum]

do you only need CHROM/POS/ID/REF/ALT or do you need the genotypes too ?

[Andrea_Bio]

i need genotypes too

[Andrea_Bio]

genotypes would be good but not essential

[Ashu]

Does any of you were able to find out the answer to this question?? I have the same problem as well :(

[Sudeep]

@Ashu I found something in this blog. Perhaps it is useful for you statsandgenomes.wordpress.com/2011/11/06/a-python-script-to-make-a-dbsnp-vcf-file/

[Ali R. Vahdati]

I have the same question

Answer 1

[Arelicorlaior]

Sudeep's comment should be the answer: http://statsandgenomes.wordpress.com/2011/11/06/a-python-script-to-make-a-dbsnp-vcf-file/

Answer 2

[Chenjy]

now, is there any tool to convert dbSNP to VCF format?

[Pierre Lindenbaum]

this should be a comment, not an answer

Answer 3

[Rituriya]

Hi, all. I found this link too - http://ngsda.blogspot.in/2011/07/mouse-dbsnp-vcf.html Maybe its already known to you guys. I wonder if it works accurately for other organisms!

Any idea?