I have been trying to use the Mutect2 of GATK toolkit, and noticed an example usage:
java -jar GenomeAnalysisTK.jar \ -T MuTect2 \ -R reference.fasta \ -I:tumor tumor.bam \ -I:normal normal.bam \ [--dbsnp dbSNP.vcf] \ [--cosmic COSMIC.vcf] \ [-L targets.interval_list] \ -o output.vcf
Here, I am assuming that the reference.fasta is the genome sequence in fasta format, and tumor.bam is the file containing details about the mapped reads. I am not sure what is normal.bam. Is it the bam file containing details of the mapped reads of a reference transcriptome with the reference genome?