gatk-workflows / gatk4-exome-analysis-pipeline
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
☆51Updated 4 years ago
Alternatives and similar repositories for gatk4-exome-analysis-pipeline:
Users that are interested in gatk4-exome-analysis-pipeline are comparing it to the libraries listed below
- Burden testing against public controls☆50Updated 10 months ago
- CNV screening and annotation tool☆24Updated 8 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆96Updated 3 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- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆66Updated 4 months ago
- ☆38Updated 11 months ago
- Relevant papers for CNV and SV approaches☆94Updated 2 months ago
- Microsatellite instability (MSI) detection for tumor only data.☆97Updated 8 months ago
- ☆21Updated this week
- Reference data: BED files, genes, transcripts, variations.☆82Updated 7 years ago
- Somatic copy variant caller (CNV) for next generation sequencing☆70Updated 4 months ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- QDNAseq package for Bioconductor☆49Updated 5 months ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- ☆108Updated last year
- ☆71Updated 8 months 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
- ☆65Updated last year
- ☆40Updated 2 years ago
- ☆51Updated 2 years ago
- ☆39Updated 8 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆69Updated 4 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years ago
- ☆78Updated 10 years ago
- Workflows for converting between sequence data formats☆37Updated 3 years ago
- Enhanced version of the FastQTL QTL mapper☆61Updated last year
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 4 years ago
- MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data☆36Updated 5 years ago