Building an indexed genome file for GATK tools

[jennaj]

Hi @jsalem

Nearly all GATK tools, including the Data Manager, as wrapped for Galaxy, are considered deprecated. These were all based on earlier releases of GATK.

Currently, the only GATK4 tool that has been wrapped is:

• GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes
• ToolShed Repository: Galaxy | Tool Shed

For native genome fasta files to be accessible to this tool (option: Choose the source for the reference list) – adding the genome with the fetch DM is probably enough, although to really make new genomes useful there is a short-list of core recommended indexes. All have Data Mangers. You can certainly run more DMs after those (GATK4 Mutect2 won’t need more… but other tools can). See the topic below for help – the same process applies to all genomes you plan to index, not just the one referenced in that particular Q&A.

Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Hi, The mm10 reference genome/build is sourced from UCSC. You’ll need to index the genome on your server with Data Manager tools. Install the genome with Data Managers (sourced from the ToolShed, all are in a separate category there). Install DMs like any other tool using the Admin functions. You’ll need these DMs at a minimum. Execute them in this order first: Fasta fetcher – has an option to pick UCSC as the data source. SAM indexer Picard indexer 2bit (twoBit) indexer Then get the DMs…