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 http://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.