✂️ ⚡ Rapid haploid variant calling and core genome alignment

Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2, as well as CSV.

Tools for querying and analysis of genomic data

Application of pan-genome for population

Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)

Learning the Variant Call Format

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Basic bioinformatics pipeline (Snakemake) to annotate VCF files with ANNOVAR

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Checks vcf files and removes loci and samples with too many missings, can also input genotypes in missing (various options for this).

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Small scripts for population genetics analysis

Calculate similarity between different samples using VCF format varaint data for IBS/IBD analysis.

Construct gene haplotype with VCF format files and snpEff annotation.

VCF: Variant Call Format files are difficult to understand at first, I already had to dive into them in order to learn how to edit them, so you can use my scripts. Some of these functions already exist in vcftools, but it seems it stopped being updated. so you can use these scripts to do various tasks with them

Genotyping of segregating mobile elements insertions

microhaplotype visualizer and analyzer

Explore and filter structural variant calls from Lumpy and Delly VCF files

Evolutionary Bioinformatics Toolkit (EBT)

It turns a VCF file into the input format for BayeScan; provided a tab-delimited population assignment file