Learning the Variant Call Format

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

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

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

BioC++ Input/Output library

A Nextflow variant normalization pipeline based on vt and bcftools

Curated cheatsheet of high-efficiency Linux, AWK, SAMtools, BCFtools, SeqKit, and Python one-liners for daily genomic data manipulation.

A collection of scripts for filtering annotated variant call format files

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

A reproducible Snakemake pipeline for the high-throughput genomic epidemiology of 96 MDR P. aeruginosa strains (BioProject PRJNA771342).

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

a Nextflow pipeline for generating imputation reference panels using 1000 Genomes and HGDP data to enhance variant calling in Blended Genome Exome sequencing

`htslib` And `bcftools` Libraries And Command Line Tools Wrapper

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

Bundled 'FastDup', 'Samtools', 'BCFtools', and 'HTSlib' Utilities

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

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

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