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 PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline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
Related projects ⓘ
Alternatives and complementary repositories for broad-prod-wgs-germline-snps-indels
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆65Updated 2 months ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years 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- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
- Snakemake-based workflow for detecting structural variants in genomic data☆77Updated 8 months ago
- QDNAseq package for Bioconductor☆48Updated 3 months ago
- An awk-like VCF parser☆54Updated 10 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- ☆78Updated 10 years ago
- R package for inferring copy number from read depth☆31Updated 2 years ago
- R package designed to simplify structural variant analysis☆69Updated 2 years ago
- Relevant papers for CNV and SV approaches☆94Updated this week
- CNV screening and annotation tool☆24Updated 8 years ago
- Lima - Demultiplex Barcoded PacBio Samples☆65Updated last week
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated 2 weeks ago
- Comprehensive benchmark of structural variant callers☆43Updated 3 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago
- Workflows for converting between sequence data formats☆37Updated 3 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- 10x Genomics Linked-Read Diploid De Novo Assembler☆64Updated 5 years ago
- ☆50Updated last year
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆55Updated 3 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆44Updated 2 years ago
- Software program for checking sample matching for NGS data☆125Updated 4 months ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆74Updated last year
- TIDDIT - structural variant calling☆69Updated 3 months ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago