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