Question: Dbsnp In Vcf Format
2
gravatar for Andrea_Bio
7.6 years ago by
Andrea_Bio2.5k
Andrea_Bio2.5k wrote:

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

vcf format dbsnp • 5.0k views
ADD COMMENTlink modified 7.4 years ago by Rituriya0 • written 7.6 years ago by Andrea_Bio2.5k

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

ADD REPLYlink written 7.6 years ago by Pierre Lindenbaum115k

i need genotypes too

ADD REPLYlink written 7.6 years ago by Andrea_Bio2.5k

genotypes would be good but not essential

ADD REPLYlink written 7.6 years ago by Andrea_Bio2.5k

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

ADD REPLYlink written 6.9 years ago by Ashu10

@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/

ADD REPLYlink written 6.8 years ago by Sudeep1.6k

I have the same question

ADD REPLYlink written 6.1 years ago by Ali R. Vahdati190
1
gravatar for Arelicorlaior
6.7 years ago by
Arelicorlaior50 wrote:

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

ADD COMMENTlink written 6.7 years ago by Arelicorlaior50
0
gravatar for Chenjy
7.2 years ago by
Chenjy0
Chenjy0 wrote:

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

ADD COMMENTlink written 7.2 years ago by Chenjy0

this should be a comment, not an answer

ADD REPLYlink written 7.2 years ago by Pierre Lindenbaum115k
0
gravatar for Rituriya
6.7 years ago by
Rituriya0
Rituriya0 wrote:

Hi, all. I foudn 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?

ADD COMMENTlink written 6.7 years ago by Rituriya0
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