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.

Using gatk on Non-human re-seq with no dbSNP & dbIndel

HubertHubert South KoreaMember

Dear the GATK team,

I'm very appreciate the gatk team.
The gatk has been very useful analysis tool for my study on human-reseq data.

I've tried using gatk on non-human re-seq data with no dbSNP & dbIndel in these days.
In that case, I found a strange result of variant calling with low QUAL value from 10 to 60. I picked up any variant with low QUAL, and looked up it in a BAM file. But that was not real variant, i think it is because there was no variant recalibration step. So i try to filter variant calling result with some value, and here is my questions.

1) As i know it, 'QUAL' means a phred-scaled quality score assigned by the variant caller. So i tried to use it to filter the variant calling result. Is there any specific filtering threshold of QUAL for non-human re-seq data?

2) By one of the post in the gatk forum, one of the GATK Dev. member said that they recommend looking at QD, not QUAL.
( http://gatkforums.broadinstitute.org/discussion/6051/how-to-interpret-a-very-broad-distribution-of-qual )
In my case, can i use QD for filtering non-human re-seq data?
And would you recommend any value and specific threshold for filtering non-human re-seq data?

Thank you in advance.

Yours respectfully,


Best Answer


Sign In or Register to comment.