The tool TAPACLOTH has been originally used in

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Scalera et al. 
Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma. 
Annals of Oncology, 2023
https://doi.org/10.1016/j.annonc.2022.12.002
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Scalera et al. 
Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Clinical Cancer Research, 2024
https://doi.org/10.1158/1078-0432.CCR-24-0626
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since then we extented and evolved TAPACLOTH to a new tool that has been named INCOMMON

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Calonaci, Krasniqi et al.
Mutation frequency and copy number alterations determine prognosis and metastatic tropism in 60,000 clinical cancer samples
https://www.medrxiv.org/content/10.1101/2024.05.13.24307238v1
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INCOMMON is available at: https://github.com/caravagnalab/INCOMMON