8000 new variant caller: MuSE · Issue #1742 · nf-core/sarek · GitHub
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new variant caller: MuSE #1742

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famosab opened this issue Dec 3, 2024 · 0 comments · Fixed by #1744 or #1829
Closed

new variant caller: MuSE #1742

famosab opened this issue Dec 3, 2024 · 0 comments · Fixed by #1744 or #1829
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enhancement New feature or request

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famosab commented Dec 3, 2024 •
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Description of feature

MuSE is a somatic point mutation caller which works with whole-genome sequencing (WGS) and whole-exome sequencing (WES) data.

This tool is unique in accounting for tumor heterogeneity using a sample-specific error model that improves sensitivity and specificity in mutation calling from sequencing data.

MuSE was used in the TCGA PanCanAtlas project2 and the ICGC Pan-Cancer Analysis of Whole Genomes (PCAWG) initiative. I would like to use it with sarek to do some follow-up analysis comparison of TCGA processed data and raw data.

The modules are already created and ready in nf-core/modules. I would try and do the integration myself.
@famosab famosab added the enhancement New feature or request label Dec 3, 2024
@famosab famosab self-assigned this Dec 3, 2024
@famosab famosab linked a pull request Dec 4, 2024 that will close this issue
feat: add MuSE as new somatic variant caller #1744
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@famosab famosab closed this as completed Mar 12, 2025
@famosab famosab linked a pull request Mar 12, 2025 that will close this issue
add muse as variant caller to images #1829
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