SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: VCF file for Local realignment around indels jorge Bioinformatics 2 10-10-2011 11:15 PM
Conflict between mpileup/bcftools and GATK in VCF file ericarcher Bioinformatics 0 09-25-2011 04:33 PM
Converting Dindel VCF file to GATK BED file MolecularToast Bioinformatics 2 09-24-2011 06:38 PM
sorting sam file crh Bioinformatics 2 06-16-2011 06:45 AM
Tool for Sorting PRB file foolishbrat Bioinformatics 1 01-26-2009 12:29 PM

Reply
 
Thread Tools
Old 06-08-2011, 10:32 AM   #1
jorge
Member
 
Location: Madrid, Spain

Join Date: Jun 2011
Posts: 25
Default GATK: sorting vcf file given a reference file

Hello,

I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

is there a canned script that allows you sort the vcf file according to a given reference sequence?

Thanks
Jorge
jorge is offline   Reply With Quote
Old 08-24-2011, 08:34 AM   #2
NGSfan
Senior Member
 
Location: Austria

Join Date: Apr 2009
Posts: 181
Default

Quote:
Originally Posted by jorge View Post
Hello,

I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

is there a canned script that allows you sort the vcf file according to a given reference sequence?

Thanks
Jorge
Buen dia Jorge, tengo un regalo para usted:

here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

enjoy!

http://code.google.com/p/vcfsorter/
NGSfan is offline   Reply With Quote
Old 08-24-2011, 11:03 PM   #3
jorge
Member
 
Location: Madrid, Spain

Join Date: Jun 2011
Posts: 25
Default

Hello,

Thanks a lot!

Jorge
jorge is offline   Reply With Quote
Old 01-26-2013, 05:08 PM   #4
bioliyezhang
Member
 
Location: Boston, MA

Join Date: Mar 2011
Posts: 19
Default

Quote:
Originally Posted by NGSfan View Post
Buen dia Jorge, tengo un regalo para usted:

here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

enjoy!

http://code.google.com/p/vcfsorter/
very useful, thanks.
bioliyezhang is offline   Reply With Quote
Old 01-14-2015, 12:16 PM   #5
bluesquid
Junior Member
 
Location: UK

Join Date: Aug 2012
Posts: 3
Default

thank you!
bluesquid is offline   Reply With Quote
Reply

Tags
fasta, gatk, reference, 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 06:40 AM.


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