Learning the Variant Call Format

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

BioC++ Input/Output library

A Nextflow variant normalization pipeline based on vt and bcftools

A collection of scripts for filtering annotated variant call format files

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

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

This script filters false positive alleles from poolseq VCF file created with bcftools.

Repository for Docker image astrabert/silly-gat-kay info and changelog

The goal of this project is to create a R package and executable scripts to visualize variants in Variant Call Format (VCF) files and Bcftools processed tab-delimited files.

pipeline: from sra, bed, vcf to plink

convert genotype array output into annotated IBD segments

The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.

This repository contains code related to a conservation genomics project focused on the king rail, a threatened marsh bird.

This directory contains material that I've used in different courses

This repository outlines steps to manage VCF files, including compressing, indexing, querying chromosomes, counting variants, and comparing multiple VCF files using BCFTools.

Merge in parallel, speeding up bcftools merge

Convert SV VCFs to BED, a wrapper for bcftools query