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!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

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 Cambridge, MAMember, Administrator, Broadie Posts: 11,421 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 Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

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

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.