Dbsnp In Vcf Format
3
2
Entering edit mode
10.7 years ago
Andrea_Bio ★ 2.7k

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

dbsnp vcf format • 6.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

i need genotypes too

ADD REPLY
0
Entering edit mode

genotypes would be good but not essential

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

@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 REPLY
0
Entering edit mode

I have the same question

ADD REPLY
1
Entering edit mode
ADD COMMENT
0
Entering edit mode
10.3 years ago
Chenjy • 0

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

ADD COMMENT
0
Entering edit mode

this should be a comment, not an answer

ADD REPLY
0
Entering edit mode
9.8 years ago
Rituriya • 0

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?

ADD COMMENT

Login before adding your answer.

Traffic: 1267 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6