SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
VCFtools Ploidy Issue ercfrtz Bioinformatics 1 11-30-2013 12:03 AM
vcfTools depth filter problem JackieBadger Bioinformatics 3 08-14-2013 08:10 AM
SNP filtering with vcftools tnguyen Bioinformatics 0 08-10-2012 04:05 AM
Problem to use Bedtools after filtering uniquely mapped reads with samtools eilosei Bioinformatics 2 12-21-2011 04:51 PM
VCFtools Vcf.pm problem - broken VCF header on 1000genomes data naumenko.sa Bioinformatics 1 07-08-2011 05:17 AM

Reply
 
Thread Tools
Old 03-20-2014, 07:06 PM   #1
Nick Bell
Junior Member
 
Location: Melbourne

Join Date: Jan 2014
Posts: 4
Default VCFtools filtering problem

I'm having some issues filtering individuals out with a GQ below a given threshold.

Using the command ./vcftools --vcf AST.txt --minGQ 10 --indv --recode
I get 0 individuals kept.

If I run it without the --indv flag it turns all my genotypes to ./.

Any ideas?
Nick Bell is offline   Reply With Quote
Old 03-21-2014, 07:00 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

Yes, because you forget to set the parameter for example: --indv NA12878
TiborNagy is offline   Reply With Quote
Old 03-22-2014, 05:29 PM   #3
Nick Bell
Junior Member
 
Location: Melbourne

Join Date: Jan 2014
Posts: 4
Default

I realise now that I misinterpreted entirely what the --indv flag meant. I wanted to filter each and every individual by it's quality, not just one!
Nick Bell is offline   Reply With Quote
Reply

Tags
depth, filtering, quality filtering, vcftools

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 04:49 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO