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Title: GitHub - babelomics/SFtool: Secondary Findings tool

Open Graph Title: GitHub - babelomics/SFtool: Secondary Findings tool

X Title: GitHub - babelomics/SFtool: Secondary Findings tool

Description: Secondary Findings tool. Contribute to babelomics/SFtool development by creating an account on GitHub.

Open Graph Description: Secondary Findings tool. Contribute to babelomics/SFtool development by creating an account on GitHub.

X Description: Secondary Findings tool. Contribute to babelomics/SFtool development by creating an account on GitHub.

Mail addresses
javier.perez.florido.sspa@juntadeandalucia.es
rosariom.carmona@juntadeandalucia.es
edurne.urrutia.lafuente@navarra.es

Opengraph URL: https://github.com/babelomics/SFtool

X: @github

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https://patch-diff.githubusercontent.com/babelomics/SFtool#secondary-findings-tool
https://patch-diff.githubusercontent.com/babelomics/SFtool#overview
https://patch-diff.githubusercontent.com/babelomics/SFtool#table-of-content
Introductionhttps://patch-diff.githubusercontent.com/babelomics/SFtool#introduction
Tool workflowhttps://patch-diff.githubusercontent.com/babelomics/SFtool##workflow
Dependencieshttps://patch-diff.githubusercontent.com/babelomics/SFtool#dependencies
Installationhttps://patch-diff.githubusercontent.com/babelomics/SFtool#installation
Usagehttps://patch-diff.githubusercontent.com/babelomics/SFtool#usage
Outputshttps://patch-diff.githubusercontent.com/babelomics/SFtool#outputs
Contributorshttps://patch-diff.githubusercontent.com/babelomics/SFtool#contributors
https://patch-diff.githubusercontent.com/babelomics/SFtool#introduction
Miller DT et al, 2023https://pubmed.ncbi.nlm.nih.gov/37347242/
Gregg AR et al., 2021https://pubmed.ncbi.nlm.nih.gov/34285390/
Klein TE et al., 2017https://ascpt.onlinelibrary.wiley.com/doi/10.1002/cpt.928
https://patch-diff.githubusercontent.com/babelomics/SFtool#tool-workflow
https://patch-diff.githubusercontent.com/babelomics/SFtool/blob/geneBePharmCAT/modules/misc/sfdiagram.png
Stawinski P et al., 2024https://onlinelibrary.wiley.com/doi/10.1111/cge.14516
see VCF requirementshttps://pharmcat.org/using/VCF-Requirements/
herehttps://pharmcat.org/Genes-Drugs/
https://patch-diff.githubusercontent.com/babelomics/SFtool#dependencies
Pythonhttps://www.python.org/
websitehttps://www.python.org/downloads
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pybedtoolshttps://daler.github.io/pybedtools/
pandashttps://pandas.pydata.org/
requestshttps://pypi.org/project/requests/
natsorthttps://pypi.org/project/natsort/
openpyxlhttps://openpyxl.readthedocs.io/en/stable/
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bcftoolshttps://samtools.github.io/bcftools/bcftools.html
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herehttps://ftp.ncbi.nlm.nih.gov/pub/clinvar/README.txt
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herehttps://hpo.jax.org/data/annotation-format
https://patch-diff.githubusercontent.com/babelomics/SFtool#installation
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https://patch-diff.githubusercontent.com/babelomics/SFtool#usage
https://patch-diff.githubusercontent.com/babelomics/SFtool#running-from-source-code
ACMG's datasethttps://www.gimjournal.org/article/S1098-3600(21)05120-0/fulltext
https://genebe.net/about/apihttps://genebe.net/about/api
https://genebe.net/about/apihttps://genebe.net/about/api
must be specifiedhttps://pharmcat.org/using/VCF-Requirements/
herehttps://github.com/PharmGKB/PharmCAT/releases
here for GRCh38 human assemblyhttps://github.com/babelomics/SFtool/blob/geneBePharmCAT/categories/PR/pr_risk_genes_GRCh38.bed
here for GRCh38 human assemblyhttps://github.com/babelomics/SFtool/blob/geneBePharmCAT/categories/RR/rr_risk_genes_GRCh38.bed
https://patch-diff.githubusercontent.com/babelomics/SFtool#running-from-singularity-image
https://patch-diff.githubusercontent.com/babelomics/SFtool#outputs
https://patch-diff.githubusercontent.com/babelomics/SFtool#final-report
herehttps://www.gimjournal.org/article/S1098-3600(23)00879-1/fulltext#tbl1
variant consequencehttps://www.ensembl.org/info/genome/variation/prediction/predicted_data.html
https://patch-diff.githubusercontent.com/babelomics/SFtool#intermediate-output-files
https://patch-diff.githubusercontent.com/babelomics/SFtool#contributors
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