Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
VQSR tag in FILTER is false positive variant ?

Hi.
I wonder whether after VQSR , the variants which have VQSR tag in FILTER column filter out, including VQSRTrancheINDEL99.00 to 99.90, VQSRTrancheINDEL99.90 to 100.00+, VQSRTrancheINDEL99.90 to 100.00, VQSRTrancheSNP99.90 to 100.00, VQSRTrancheSNP99.90 to 100.00+? These means are false positive variants?
and What do 100.00+ mean?
Can I have Only "PASS" variants tin FILTER tab as true positve variant ?
Tagged:
Answers
@Sunhye
Hi,
Can you tell me what version of GATK you are using and the exact commands you ran in the VQSR step?
Also, please post some example records from your output VCF.
Thanks,
Sheila
Hi @Sheila !
My GATK version is 3.4-46-gbc02625.
My commands is,
Finally, vcf recode is,
@Sunhye
Hi,
Those VQSLOD score do not look good. Can you post the tranche plots and recalibration plots?
Thanks,
Sheila
Hi @Sheila
I'm so sorry my late reply.
For chr4.recal.vcf, I attach files about the tranche plots and recalibration plots.
Could you check these files?
And I wonder that about variant filtering, VQS LOD value should use than than the presence or absence of the VQSR tag in filter colum to filter variant?
If so, what is VQS LOD's range to decide filtering ?
@Sunhye
Hi,
Sorry for the late response. Can you tell me more about your samples and how you ran VQSR? How many samples do you have and are they whole genome or whole exome?
Thanks,
Sheila
@Sunhye I'm not sure I will be of much help, but here goes. I noticed this part of your command:
Preferably you should run VR across all chromosomes simultaneously/concurrently.
You should filter on truth sensitivity tranches; not on VQSLOD values.
It is described in your VCF header, which VQSLOD values this corresponds to:
It depends what TS threshold you use, when you run ApplyRecalibration.
Hi @Sheila .
My samples are 62 individuals and whole genome sequencing.
And How to run VQSR is followed by GATK best practice.
For SNP,
For Indel,
Hi @tommycarstensen !
Thanks for your detailed comment!
Your reply are very helpful to me!