SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
extract data from fasta-files with perl?? anna_ Bioinformatics 20 02-17-2016 07:29 AM
Extract fastq files of unaligned reads with Bowtie 2 Mad4Seq Bioinformatics 4 06-19-2013 09:53 PM
how to combine .gz files and extract? ibn.adam RNA Sequencing 1 10-04-2011 06:49 AM
using vcf tools to extract genotype information rna_seeker Bioinformatics 3 07-10-2011 05:25 PM
Any program to extract different peaks from two wigs files hon Bioinformatics 1 10-29-2009 01:30 AM

Reply
 
Thread Tools
Old 11-21-2011, 10:19 AM   #1
liu_xt005
Member
 
Location: Iowa City, IA

Join Date: Jun 2011
Posts: 24
Question Extract Infor from 1000G VCF files

I wonder if anyone can teach me a simple way to extract specific information (e.g. "LCSNP', 'LDAF', etc) of the variants from 1000 genome variant 2011 Oct release? The 'INFO' field is compressed in one single column, consisting of non-constant number of terms separated by semicolon ";". Perl matching is not efficient at all.
liu_xt005 is offline   Reply With Quote
Old 11-21-2011, 01:33 PM   #2
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

Why is PERL matching not efficient. Loading a variable number of delimited elements into an array is just the kind of thing PERL was designed for...

Other than writing your own scripts, you might try:
http://vcftools.sourceforge.net/
adaptivegenome 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 09:02 AM.


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