bcftools
There are 0 repository under bcftools topic.
davetang / learning_vcf_file
Learning the Variant Call Format
Language:Perl 137digo4 / Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Language:Shell 37mnievesc / Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Language:Shell 9PavlidisLab / bioluigi
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
Language:Python 9- Language:C++ 8
TRON-Bioinformatics / tronflow-vcf-postprocessing
A Nextflow variant normalization pipeline based on vt and bcftools
Language:Shell 5RhettRautsaw / VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Language:Python 4scholl-lab / vcf-filtering
A collection of scripts for filtering annotated variant call format files
Language:Shell 4sdhutchins / vcf-prepping
Scripts used on a cluster that demonstrate vcf file manipulation and preparation.
Language:Shell 3- Language:Jupyter Notebook 2
AstraBert / silly-gat-kay
Repository for Docker image astrabert/silly-gat-kay info and changelog
Language:Dockerfile 2ozankiratli / FilteringFalsePositives
This script filters false positive alleles from poolseq VCF file created with bcftools.
Language:Shell 2yenon118 / VisualVariants
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.
Language:R 21tilly / wgs-exercise
The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.
Language:Python 1biodata-fun / course_material
This directory contains material that I've used in different courses
- KingRailPopGen
gausec / KingRailPopGen
This repository contains code related to a conservation genomics project focused on the king rail, a threatened marsh bird.
Language:Shell 1 openb-io / ibd-pipeline
convert genotype array output into annotated IBD segments
Language:Shell 10-Ioniel-0 / guppy_MR
Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.
Language:Python 0adrianodemarino / bcftools_merge_parallel
Merge in parallel, speeding up bcftools merge
Language:Shell 0CHRUdeLille / bcftools_containers
bcftools singularity container
Language:Shell 0gibsonMatt / bioneer
a tool for quickly getting the correct bcftools command
Language:Python 0maurya-anand / liftover
Convert genomic coordinates from the Human Genome version 19 (hg19) to version 38 (hg38)
Language:Makefile 0nglaz0v / P-aeruginosa_antibiotic-resistance_copper
:microscope: Влияние меди на антибиотикорезистентность у синегнойной палочки
Language:HTML 0nicolo-tellini / S.cerevisiaeData
1,674 S.cerevisiae genomics data
Language:Shell 0cnr-ibba / nf-resequencing-mem
Nextflow resequencing pipeline with bwa-mem and freebayes
Language:Nextflow- Language:Python
GiatrasKon / Chromosome11-VariantCalling-GATK
A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.
Language:ShellGrelot / reserveBenefit--snpsdata_analysis
Codes i wrote for the paper "genomic resources for Mediterranean fishes"
Language:ShellJoshua-Jandrell / Genome_Visualiser
Code final year dynamic genome visualizer project.
Language:Pythonjubayer98 / VCF-Toolkit
This repository outlines steps to manage VCF files, including compressing, indexing, querying chromosomes, counting variants, and comparing multiple VCF files using BCFTools.
Language:Shell
