gatk-workflows / broad-prod-wgs-germline-snps-indelsLinks
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 PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline
☆57Updated 5 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
Sorting:
- Documenting usage and experience with bioinformatic tools☆40Updated 10 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆55Updated 5 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆78Updated 5 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆99Updated 3 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 5 years ago
- Characterization of Germline variants☆99Updated 3 years ago
- 10x Genomics Linked-Read Diploid De Novo Assembler☆65Updated 7 years ago
- R package designed to simplify structural variant analysis☆74Updated 4 years ago
- R Package for Non Invasive Prenatal Testing (NIPT) analysis☆44Updated 6 years ago
- R package for inferring copy number from read depth☆32Updated 3 years ago
- My bioinfo toolbox☆50Updated 10 months ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆75Updated last year
- Tip and tricks for BAM files☆86Updated 7 years ago
- ClassifyCNV: a tool for clinical annotation of copy-number variants☆69Updated 2 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆53Updated 3 years ago
- Precision HLA typing from next-generation sequencing data☆75Updated last week
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆47Updated 7 years ago
- ☆69Updated 3 years ago
- Workflows for converting between sequence data formats☆40Updated 4 years ago
- identifying mutational significance in cancer genomes☆62Updated 3 years ago
- ☆57Updated 5 years ago
- Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data☆91Updated 3 months ago
- A simplified pipeline for ctDNA sequencing data analysis☆37Updated 8 years ago
- Relevant papers for CNV and SV approaches☆94Updated last year
- ☆54Updated 2 years ago
- Runs a combination of tools to generate structural variant calls on whole-genome sequencing data☆103Updated 5 years ago
- phasing and Allele Specific Expression from RNA-seq☆117Updated last year
- ☆43Updated last year
- Concordance and contamination estimator for tumor–normal pairs☆59Updated last year
- FEELnc : FlExible Extraction of LncRNA☆92Updated 5 months ago