gatk-workflows / broad-prod-wgs-germline-snps-indels
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline
☆55Updated 4 years ago
Alternatives and similar repositories for broad-prod-wgs-germline-snps-indels:
Users that are interested in broad-prod-wgs-germline-snps-indels are comparing it to the libraries listed below
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆51Updated 4 years ago
- QDNAseq package for Bioconductor☆49Updated 5 months ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Comprehensive benchmark of structural variant callers☆44Updated 3 years ago
- R package designed to simplify structural variant analysis☆71Updated 3 years ago
- ☆78Updated 10 years ago
- CNV screening and annotation tool☆24Updated 8 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆66Updated 4 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆96Updated 3 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆79Updated 11 months ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆76Updated 4 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆20Updated 2 years ago
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆26Updated last year
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Workflows for converting between sequence data formats☆37Updated 3 years ago
- Burden testing against public controls☆50Updated 10 months ago
- CN-Learn☆29Updated 4 years ago
- ☆38Updated 11 months ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- ☆39Updated 8 months ago
- Relevant papers for CNV and SV approaches☆94Updated 2 months ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆45Updated 2 years ago
- Battenberg R package for subclonal copynumber estimation☆83Updated 2 months ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- an empirical Bayesian framework for mutation detection from cancer genome sequencing data☆31Updated 8 years ago
- ☆51Updated 2 years ago
- Helper scripts for biological data processing from Sentieon☆64Updated 2 months ago
- R Package for Non Invasive Prenatal Testing (NIPT) analysis☆41Updated 5 years ago