IndelRealign mitochondrial DNA using b37

Question

[Cindy]

I want to run GATK IndelRealigner for mtDNA and use b37 indel reference as known sites. Here is my script. I got error for incompatible contigs. The NC_012920.1.fasta is mitochondria reference genome and includes only M contigs. How can I modify it to make it compatible to b37 indel reference genome? Thanks!

java  -jar GenomeAnalysisTK.jar \
         -R NC_012920.1.fasta \
     -T IndelRealigner \
     -targetIntervals file_GATKrealign.intervals \
     -I file \
      -o file_realn.bam \
      -known b37/1000G_phase1.indels.b37.vcf \
     -known b37/Mills_and_1000G_gold_standard.indels.b37.vcf

##### ERROR MESSAGE: Input files b37/1000G_phase1.indels.b37.vcf and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: No overlapping contigs found.
##### ERROR   b37/1000G_phase1.indels.b37.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X]
##### ERROR   reference contigs = [M]

Answer 1

[Jeremy Leipzig]

The problem is likely naming related (M vs MT) but the bigger issue is that this GATK realignment approach is really overkill for mitochondria sequences. You could easily do a real alignment using BLAST or something else more sensitive. There are no mitochondrial gold standard indels in your references anyway.