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.

Different versions of MT used in Mills_and_1000G indels in the GATK_b37_bundle resource bundle?

WimSWimS Member Posts: 27
edited August 2013 in Ask the GATK team

I mapped data against the human reference provided in the GATK_b37_bundle resource bundle and I am now trying to run BQSR using the recommended known variant sets from the same resource bundle.

Upon including the Mills_and_1000G_gold_standard.indels.b37.vcf known variant set I get the following error:

##### ERROR contig knownSites = MT / 16571
##### ERROR contig reference = MT / 16569

The header of the Mills_and_1000G_gold_standard.indels.b37.vcf seems to the indicate that the correct 16569 bp MT version is used for the VCF file

##contig=<ID=MT,length=16569,assembly=b37>

Why does the BQSR tool think that a different version of MT is used for the Mills_and_1000G_gold_standard.indels.b37.vcf ?

Edit:

I have the same problem with the 1000G_phase1.indels.b37.vcf from the GATK_b37_bundle. Get the same error and the MT contig seems the be the correct one from the vcf header. Only the dbsnp_137.b37.vcf is accepted by the BQSR tool without complaining about a different MT contig.

Tagged:

Best Answer

Answers

  • WimSWimS Member Posts: 27

    I'll remove the indexes or download the files again. Thanks for checking at your side.

Sign In or Register to comment.