Full GATK SNP calling pipeline
☆24Oct 30, 2025Updated 9 months ago
Alternatives and similar repositories for gatk-snp-calling
Users that are interested in gatk-snp-calling are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Code associated with the manuscript "A complete reference genome improves analysis of human genetic variation".☆17Jan 17, 2023Updated 3 years ago
- Gene Prediction using MAKER, CEGMA, SNAP, GENEMARK & AUGUSTUS☆10Jul 20, 2017Updated 9 years ago
- Various scripts that I have created that are useful for genome annotation (repeats & proteins)☆17Feb 21, 2022Updated 4 years ago
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 5 years ago
- Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as p…☆11Jun 25, 2019Updated 7 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated 2 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 7 months ago
- Imputation-beagle-tutorial☆39Jun 2, 2022Updated 4 years ago
- Perform GWAS with gemma in a simple pipeline☆27Apr 26, 2025Updated last year
- MODAS: Multi-Omics Data Association Study toolkit☆21Nov 21, 2024Updated last year
- Preprocessing sequencing data for allele-specific analysis☆13Mar 11, 2025Updated last year
- A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framewor…☆33Mar 18, 2014Updated 12 years ago
- Plotly BioVisualization 🎯 Interactive Needle and Manhattan Plots & Alignment Viewer☆11Feb 28, 2020Updated 6 years ago
- ☆12Dec 1, 2020Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- De novo lncRNA discovery pipeline, re-write of PLAR in shell and awk☆10Aug 2, 2023Updated 3 years ago
- A tool to visualize the haplotype pattern and various information in excel.☆24Mar 5, 2025Updated last year
- Set of script for the paper on the cattle graph genome☆14Jan 10, 2023Updated 3 years ago
- Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using…☆29Jul 8, 2026Updated last month
- A toolkit for identifying recombination and recombinant genotypes☆26Dec 3, 2025Updated 8 months ago
- Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣☆11Apr 28, 2023Updated 3 years ago
- ☆18Nov 26, 2023Updated 2 years ago
- Scripts for analysis used during the course☆98Apr 30, 2024Updated 2 years ago
- ☆12Jun 12, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- scripts for sequence and feature conversion, annotation, analysis ...☆28Mar 17, 2025Updated last year
- Accurate haplotype construction and detection of selection signatures enabled by 889 high quality pig genome sequences☆14May 11, 2023Updated 3 years ago
- A graduate-level elective course: Python Programming for Life Science Students☆10Mar 26, 2026Updated 4 months ago
- A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes☆30Apr 10, 2024Updated 2 years ago
- ☆10Feb 25, 2024Updated 2 years ago
- 基因组组装注释流程及脚本☆15Feb 12, 2023Updated 3 years ago
- A Python package with integrated lncRNA prediction methods☆13Feb 17, 2021Updated 5 years ago
- ☆13Mar 22, 2022Updated 4 years ago
- In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Pra…☆16Oct 16, 2019Updated 6 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A new simple and efficient software to PCA and Cluster For popolation VCF File☆83Aug 1, 2026Updated last week
- The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).☆21Sep 9, 2021Updated 4 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Genome Annotation Pipeline☆45Aug 20, 2024Updated last year
- tips and tricks in genome-wide association studies - a tutorial☆14Jul 25, 2023Updated 3 years ago
- a Semi-automated pipeline for assembling T2T genome☆28Oct 16, 2025Updated 9 months ago
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆15Nov 20, 2023Updated 2 years ago