Bowtie2 hg19 reference for gatk MuTect

Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and using hg19 Bowtie2 index from bowtie-bio.sourceforge.net/bowtie2/index.shtml gives a compatibility error with dbsnp_138.hg19.vcf file while running GATK MuTect.

ERROR MESSAGE: Input files dbsnp_138.hg19.vcf and reference have incompatible contigs: No overlapping contigs found.

Is there any way to fix this other than switching to the bwa aligner? Is there a different reference or dbsnp vcf file I could use? Thank you for your help.

Since GATK does not provide a Bowtie2 index, the index does not exist. Thus, you need to generate it yourself.

Do I need to create new indices to be able to use this reference file from the GATK bundle with bowtie2?

Yes, creating the bowtie2 indices would help.

Input files dbsnp_138.hg19.vcf and reference have incompatible contigs

Okay, so did you do the obvious thing and check to see that chromosome names are the same between the two files?