Syntax highlighting for computational biology

The powerful `awk` script to calculate pi, Dxy and Fst in polyploid VCF files with mixed-ploidy groups support

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.

A Nextflow variant normalization pipeline based on vt and bcftools

A collection of scripts for filtering annotated variant call format files

Variant annotation and filtration server ALAPY Genome Explorer

Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

A Bioinformatics pipeline to process Raw reads to VCF files in Bash

convert genotype array output into annotated IBD segments

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

🧬 Open-source genetic analysis toolkit. Analyze your WGS/VCF data locally and privately. 500+ variants across fitness, health, traits & more. For education & fun only - not for clinical use.

Variant discovery pipeline

Calling SNPs using TASSEL GBS V2 pipeline for ponderosa pine using the reference genome of loblolly pine

A bash script based pipeline to analyze Rad-seq data to get SNPs.

Built around the vcf2tsv software. Make a tsv from a vcf for the excel lovers in your life.

This script automates missense SNP extraction/counting from VCF files using BCFTools. Processes multiple samples, handles compressed formats, verifies dependencies, and generates standardized reports for genomic variant analysis