The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

Combine 2 VCF with different references

d_nid_ni Member Posts: 17

Hello!

So today I have to compare two different vcf (from different pipelines, only one of them is from GATK) and when I tried to combine it with combineVariants, I had an error because the references doesn't match:

The provided variant file(s) have inconsistent references for the same position(s) at chr1:1724719, A* vs. G*

I know why it's happening, but I don't know if there is an option/tools to "fix" the vcf from the other pipeline.

That I want to do is take the VCF created with a "bad" reference and use a command or GATK option to "fix" it according with the correct reference fasta file.

Thanks for your help!

Tagged:

Best Answer

Answers

  • d_nid_ni Member Posts: 17

    It doesn't solve my problem, because I don't know which is the original reference... but maybe useful for other.

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,134 admin

    Have you checked the VCF header? Depending on the tool that created it it might contain reference information.

    Geraldine Van der Auwera, PhD

  • d_nid_ni Member Posts: 17

    Hi Geraldine,

    I created this vcf by myself with custom scripts from microarray data, so finally, I changed my code to check the reference (the same as I use for GATK) and now it's working fine.

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,134 admin

    Great, always glad to hear when a problem goes away :)

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.