gatk-workflows / gatk4-somatic-cnvs
This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
☆43Updated 5 years ago
Alternatives and similar repositories for gatk4-somatic-cnvs:
Users that are interested in gatk4-somatic-cnvs are comparing it to the libraries listed below
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- Characterization of Germline variants☆98Updated 3 years ago
- Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools☆51Updated 5 years ago
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆97Updated 2 years ago
- ☆53Updated 2 years ago
- Burden testing against public controls☆50Updated last year
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆68Updated 7 months ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆80Updated 4 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆46Updated last week
- ☆41Updated last year
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Updated 9 months ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆56Updated 4 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 7 years ago
- FusionInspector code☆57Updated 5 months ago
- QDNAseq package for Bioconductor☆50Updated 8 months ago
- ☆36Updated 4 years ago
- ⛏ HLA predictions from NGS shotgun data☆53Updated last week
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- ClassifyCNV: a tool for clinical annotation of copy-number variants☆62Updated last year
- Battenberg R package for subclonal copynumber estimation☆86Updated 3 weeks ago
- ☆21Updated last week
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆28Updated last year
- ☆25Updated 5 years ago
- CNV screening and annotation tool☆25Updated 8 years ago