SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Best place to get .vcf with genotypes for HapMap cell lines? albireo Bioinformatics 0 06-13-2013 03:19 AM
How to convert hapmap file to QTL Cartographer format shuang Bioinformatics 0 03-11-2013 07:41 AM
Where can I get GM19240 HapMap cell line variant calls as VCF or a BED file adrian Bioinformatics 2 09-13-2012 01:27 AM
How to convert VCF to PED emilyjia2000 Bioinformatics 0 12-19-2011 01:39 PM
convert vcf into bed format nans_bn Bioinformatics 0 08-01-2011 11:34 PM

Reply
 
Thread Tools
Old 03-06-2015, 05:43 AM   #1
sandesh
Member
 
Location: TN

Join Date: Jun 2013
Posts: 17
Default convert vcf to hapmap

I was trying to use SNPhylo software.
I needed to combine multiple SNP vcf files together or use combined hapmap file.
Is there any way to get single vcf or hapmap file with multiple samples together?
sandesh is offline   Reply With Quote
Old 03-06-2015, 05:58 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,888
Default

bcftools-merge? http://vcftools.sourceforge.net/htslib.html#merge
GenoMax is online now   Reply With Quote
Old 03-11-2015, 05:58 AM   #3
sandesh
Member
 
Location: TN

Join Date: Jun 2013
Posts: 17
Default

Quote:
Originally Posted by GenoMax View Post


Thanks I tried vcf-merge
sandesh is offline   Reply With Quote
Old 02-15-2016, 11:13 PM   #4
lalchung
Junior Member
 
Location: INDIA

Join Date: Feb 2016
Posts: 2
Default

@sandesh
i am trying to run SNPhylo.do i need all the VCF, Simple SNP file and hapmap file ??or i need just one of these files.pls help
lalchung is offline   Reply With Quote
Old 02-16-2016, 05:01 AM   #5
yzzhang
Member
 
Location: florida

Join Date: Jan 2013
Posts: 66
Default

I fed SNPhylo only a VCF file and it ran smoothly. If you use SNPhylo, please check the sam headers, it seems SNPhylo only accept number as chromosome header (e.g. >1 but not >chr1) at least for old SNPhylo version (2014.....). Hope it helps.
yzzhang is offline   Reply With Quote
Old 02-16-2016, 07:06 AM   #6
lalchung
Junior Member
 
Location: INDIA

Join Date: Feb 2016
Posts: 2
Default SNPhylo

hi yzzhang, i appreciate your help. I have this project to find SNPs across 5 different population and build a phylogenetic tree. so, for my VCF file should i combine all the SNPs from all population into one VCf file and then run SNPhylo??
lalchung is offline   Reply With Quote
Reply

Tags
hapmap, snphylo, vcf

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 06:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO