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Bam files for MuTect
Are the requirements for the BAM files the same for MuTect as for GATK.
I have the tumor and normal bam files and they are co-ordinate sorted, indexed and aligned to MM9 using TopHat.
I have the snp vcf file as well as the reference fasta file in order. But, When i run muTect I get an error saying BAM files are not indexed. Can anyone help suggest me what should I try next?.