gatk-workflows / gatk4-jupyter-notebook-tutorials
This repository contains Jupyter Notebooks containing GATK Best Practices Workflows
☆26Updated 5 years ago
Alternatives and similar repositories for gatk4-jupyter-notebook-tutorials:
Users that are interested in gatk4-jupyter-notebook-tutorials are comparing it to the libraries listed below
- Clinical interpretation of somatic mutations in cancer☆44Updated 2 years ago
- ClassifyCNV: a tool for clinical annotation of copy-number variants☆60Updated last year
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆43Updated 2 years ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆76Updated 2 months ago
- optimization of ribosome P-site positioning in ribosome profiling data☆47Updated last year
- Identifying recurrent mutations in cancer☆37Updated 3 years ago
- EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.☆56Updated 2 months ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated this week
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated this week
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- Burden testing against public controls☆50Updated 11 months ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆67Updated 5 months ago
- An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.☆4Updated last year
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆41Updated 2 weeks ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆33Updated 7 months ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 6 years ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 2 years ago
- ☆68Updated 2 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 4 years ago
- CN-Learn☆29Updated 5 years ago
- Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data☆34Updated 2 months ago
- Generic human DNA variant annotation pipeline☆57Updated last year
- Tumor Mutational Burden☆57Updated 5 months ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆34Updated 3 years ago
- ☆20Updated last week
- simple comparison of snakemake, nextflow and cromwell/wdl☆50Updated 4 years ago