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nf-core · Dec 10, 2024 · 532902a · 532902a
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 | [Control-FREEC](https://github.com/BoevaLab/FREEC)                                                      |  x  |  x  |   x    |     -     |     x      |           x            |
 | [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro)                                             |  x  |  x  |   x    |     -     |     -      |           x            |
 
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 ## How to run ASCAT with whole-exome sequencing data?
 
 ASCAT runs out of the box on whole genome sequencing data using iGenomes resources. While the ASCAT implementation in sarek is capable of running with whole-exome sequencing data, the needed references are currently not provided with the igenomes.config. According to the [developers](https://github.com/VanLoo-lab/ascat/issues/97) of ASCAT, loci and allele files (one file per chromosome) can be downloaded directly from the [Battenberg repository](https://ora.ox.ac.uk/objects/uuid:08e24957-7e76-438a-bd38-66c48008cf52).