SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Direction/Orientation of Illumina read in SAM file flobpf Bioinformatics 3 11-12-2013 03:06 AM
Changing strand orientation in VCF files sagi.polani Bioinformatics 2 08-29-2013 12:51 AM
multiple vcf files to one multisampled vcf file Jetse Bioinformatics 2 06-27-2013 05:34 AM
How to get list of column in vcf file using Vcf.pm? jessada Bioinformatics 0 01-20-2012 07:22 AM
Strand orientation after tophat mapping Inti RNA Sequencing 0 10-12-2011 03:11 AM

Reply
 
Thread Tools
Old 01-31-2014, 10:41 AM   #1
Nino
Member
 
Location: New York City

Join Date: Mar 2013
Posts: 27
Default Strand orientation from VCF file

Hello,

I am trying to figure out how I can get the strand orientation of each call made on a snp.vcf file. Does anyone know of a way?

In the end I am looking for this in one file complete file.
chr strt end ref alt strnd_orient(+/-) associated_gene

I have tried using this Bedtools command but was not successful
intersectBed -a Benign.vcf -b ucscRetro_hg19.bed -header -wao 1> test


Thanks,
Nino
Nino is offline   Reply With Quote
Old 01-31-2014, 11:34 AM   #2
vivek_
PhD Student
 
Location: Denmark

Join Date: Jul 2012
Posts: 164
Default

I think all reported calls are assumed to be on the forward strand in VCF specification.
vivek_ 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 09:16 AM.


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