SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK UnifiedGenotyper calling way too many SNPs in vcf swbarnes2 Bioinformatics 0 08-17-2011 01:33 PM
Bovine SNPs in VCF format????? HELP! AKilleen Bioinformatics 1 05-10-2011 01:54 PM
Calling multiple BAM files for SNPs and vcf newbietonextgen Bioinformatics 3 04-19-2011 11:29 AM
Predicting true SNPs from .vcf file swbarnes2 Bioinformatics 1 04-06-2011 03:29 PM
Korean "Hanwoo" bovine genome and whole SNPs announced CLC bio Vendor Forum 0 01-28-2010 12:53 PM

Reply
 
Thread Tools
Old 05-10-2011, 05:03 AM   #1
Moo
Junior Member
 
Location: Ireland, Meath

Join Date: May 2011
Posts: 3
Unhappy VCF formated bovine SNPs

Does anybody know if and how I can access a list of all reported bovine SNPs in VCF format?
Moo is offline   Reply With Quote
Old 05-10-2011, 05:45 AM   #2
KNS
Member
 
Location: CH

Join Date: Aug 2010
Posts: 17
Default

Yes, vcf files can always be viewed from an editor. Check
http://samtools.sourceforge.net/mpileup.shtml
for what the columns mean.
HTH
KNS is offline   Reply With Quote
Old 05-10-2011, 06:07 AM   #3
sdvie
Member
 
Location: Spain

Join Date: Jul 2010
Posts: 68
Default

It is not vcf format, but maybe it helps, though:

The dbSNP Build 133 for cow (txid 9913) was recently announced on the dbSNP site

check the readme file here for all downloadable files.

cheers,
Sophia
sdvie is offline   Reply With Quote
Old 05-23-2011, 05:01 AM   #4
Moo
Junior Member
 
Location: Ireland, Meath

Join Date: May 2011
Posts: 3
Default

Cheers for the reply guys! It's looking like we're going to convert the files to .bed format instead
Moo is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:51 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO