ClairS - a deep-learning method for long-read somatic small variant calling
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Updated
Jul 5, 2024 - Python
ClairS - a deep-learning method for long-read somatic small variant calling
Clinical Whole Genome and Exome Sequencing Pipeline
An ensemble approach to accurately detect somatic mutations using SomaticSeq
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…
Pipeline for Somatic Variant Calling with WES and WGS data
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Snakemake-based workflow for detecting structural variants in genomic data
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
A Platypus-based workflow for indel calling
Super fast conversion of GVF file format to VCF file format
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
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