The current GATK version is 3.3-0

#### Howdy, Stranger!

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

Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.

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

Posts: 25Member
edited August 2013

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.