SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 12:16 PM
VCFtools Vcf.pm problem - broken VCF header on 1000genomes data naumenko.sa Bioinformatics 1 07-08-2011 04:17 AM
failed when merging the example VCF files using VCFtools jianfeng.mao Bioinformatics 1 02-02-2011 05:44 PM
failed annotating the example vcf file in the installation folder of VCFtools jianfeng.mao Bioinformatics 0 01-06-2011 05:23 AM
vcftools typical usage dawe Bioinformatics 1 08-13-2010 05:40 AM

Reply
 
Thread Tools
Old 01-20-2012, 04:00 AM   #1
shawpa
Member
 
Location: Pittsburgh

Join Date: Aug 2011
Posts: 72
Default sorting vcf- can't get vcftools to work

I am trying to run CountCovariates in GATK. I downloaded the most recent dbsnp file from the broad institute site. The problem is it is not sorted in chromosomal order. I have vcf-tools installed and tried to sort using the -c command. It is telling me "Obsolete version of sort command installed, please run without the -c option." But, if I type in vcf-sort -h , the usage says the -c is available. I have checked to make sure we have the most recent version. I don't find the vcf-tools website to be very helpful. Could someone point me in the right direction or do you know where I can download a sorted vcf file? Is there another program that I can use?
shawpa is offline   Reply With Quote
Old 01-20-2012, 04:46 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

I'm not sure which version of vcf-tools you have. The most recent one (0.1.7) doesn't have a -c option for vcf-sort. Perhaps try updating vcf-tools.
dpryan is offline   Reply With Quote
Old 01-25-2012, 05:18 AM   #3
Petr
Junior Member
 
Location: Europe

Join Date: Oct 2011
Posts: 6
Default

The -c works only on system with newer unix sort commands which support the --version-sort option.
Petr 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 01:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO