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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?.