genome / analysis-workflows
Open workflow definitions for genomic analysis from MGI at WUSM.
☆102Updated 4 months ago
Related projects ⓘ
Alternatives and complementary repositories for analysis-workflows
- Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls☆192Updated 3 years 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
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆69Updated 4 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- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
- Documentation and description of AWS iGenomes S3 resource.☆107Updated 4 years ago
- Script to automatically create and run IGV snapshot batchscripts☆137Updated last year
- microsatellite instability detection using tumor only or paired tumor-normal data☆126Updated 3 years ago
- Finder of Somatic Fusion Genes in RNA-seq data☆142Updated last year
- Software program for checking sample matching for NGS data☆125Updated 5 months ago
- Call and score variants from WGS/WES of rare disease patients.☆90Updated this week
- Workflows for converting between sequence data formats☆37Updated 3 years ago
- ☆81Updated 5 years ago
- VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.☆94Updated 6 months ago
- Microassembly based somatic variant caller for NGS data☆154Updated 2 years ago
- ABRA2☆91Updated last year
- Workflows for germline short variant discovery with GATK4☆133Updated 3 years ago
- A collection of reusable WDL tasks. Category:Other☆85Updated this week
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 4 years ago
- A structural variation pipeline for short-read sequencing☆171Updated this week
- Microsatellite instability (MSI) detection for tumor only data.☆94Updated 6 months ago
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆142Updated last year
- ASCAT R package☆170Updated 3 weeks ago
- Annotation and Ranking of Structural Variation☆221Updated 2 months ago
- ☆19Updated this week
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆154Updated last year
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆152Updated 2 months ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- VarDict☆187Updated 10 months ago
- Relevant papers for CNV and SV approaches☆94Updated 2 weeks ago