SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using GATK's local realigner outside of GATK pipeline for variant calling NikTuzov Bioinformatics 1 09-08-2015 08:41 AM
VariantFiltration weird error francois.sabot Bioinformatics 0 12-11-2011 11:26 PM
GATK VariantFiltration undefined variable AB wanguan2000 Bioinformatics 0 08-03-2011 05:52 PM

Reply
 
Thread Tools
Old 01-25-2017, 04:37 AM   #1
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default Alternative to GATK's VariantFiltration

Hello,

as I'm working in a business company I'm not allowed to use GATK without a expensive license. So I'm looking for an alternative for GATK's VariantFiltration module.

What I'm searching is a simply way to add values to the FILTER field due to values (or calculated values) from the INFO and FORMAT annotations.

Thanks for any advice.

fin swimmer
finswimmer is offline   Reply With Quote
Old 01-27-2017, 01:59 AM   #2
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default

SnpEff seems to do what I wanted.

It seems that I cannot add more than one filter at time and have to run it for every filter again on the newly created vcf file. But that's ok for now.

I'm happy to hear about other solutions.

fin swimmer
finswimmer is offline   Reply With Quote
Old 01-27-2017, 02:15 AM   #3
vivek_
PhD Student
 
Location: Denmark

Join Date: Jul 2012
Posts: 164
Default

If hard filtering is what you want to do, you can simply write scripts to parse the VCF and either modify the QUAL column in the VCF or simply exclude variants.

However the GATK's variant filtering recommendation is VQSR which uses machine learning to classify variants using known sets. I've not come across something similar from any other tool kit.
vivek_ is offline   Reply With Quote
Old 01-27-2017, 02:40 AM   #4
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default

Of course it's not that hard to parse a vcf file. But if there is something commonly used out there, it's much less error prone.

VQSR is nothing I can use here, because I'm doing targeted resequencing and not whole-genome or exom sequencing. So not enough data.

fin swimmer
finswimmer is offline   Reply With Quote
Old 02-14-2017, 08:02 PM   #5
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default

bcftools is doing this job also very nice, with the benefit I can use pipes. So intermediate files arent't needed.
finswimmer 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 07:34 PM.


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