stjudecloud / workflowsLinks
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
☆36Updated this week
Alternatives and similar repositories for workflows
Users that are interested in workflows are comparing it to the libraries listed below
Sorting:
- A python package and a set of shell commands to handle GTF files☆48Updated 11 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- for visual evaluation of read support for structural variation☆54Updated last year
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆47Updated this week
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆75Updated 10 months ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆45Updated 2 years ago
- Create WDL documentation using Markdown.☆27Updated last week
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 3 months ago
- CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.☆39Updated last month
- B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework☆60Updated last month
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 5 years ago
- A snakemake pipeline for SV analysis from nanopore genome sequencing☆51Updated 5 years ago
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- Portable WDL workflows for IDseq production pipelines☆31Updated 3 years ago
- Cancer Predisposition Sequencing Reporter (CPSR)☆59Updated last month
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- Mapped QC analysis program☆44Updated 7 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Updated 4 years ago
- Gene Fusion Visualiser☆51Updated 2 years ago
- A nextflow pipeline to perform state-of-the-art genome-wide association studies.☆67Updated 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…☆53Updated 4 years ago
- Reference genome resource manager☆76Updated last year
- An awk-like VCF parser☆56Updated last year
- Genomes on the Cloud, Mapping & Variant Calling Pipelines☆34Updated 8 years ago
- ☆69Updated last year
- Mutation Identification Pipeline. Read the latest documentation:☆44Updated last year
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- FusionInspector code☆57Updated 2 weeks ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆50Updated 3 years ago