GitHub topics: bcftools
LilValero/Human-Exome-Variant-calling-Using-Illumina-Data
Bioinformatics pipeline for Illumina human exome variant calling using FastQC, Trimmomatic, BWA, Samtools, Bcftools, and SnpEff. Demonstrates a reproducible workflow for NGS data analysis. #bioinformatics #genomics #variant-calling #ngs #pipeline
Language: HTML - Size: 638 MB - Last synced at: about 22 hours ago - Pushed at: about 23 hours ago - Stars: 0 - Forks: 0
davetang/learning_vcf_file
Learning the Variant Call Format
Language: Perl - Size: 42.6 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 139 - Forks: 40
PavlidisLab/bioluigi
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
Language: Python - Size: 120 KB - Last synced at: 23 days ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 0
cnr-ibba/nf-resequencing-mem
Nextflow resequencing pipeline with bwa-mem and freebayes
Language: Nextflow - Size: 2.66 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
TRON-Bioinformatics/tronflow-vcf-postprocessing
A Nextflow variant normalization pipeline based on vt and bcftools
Language: Shell - Size: 10.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1
scholl-lab/variantcentrifuge
A pipeline for filtering annotated variant call format files
Language: Python - Size: 288 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
scholl-lab/vcf-filtering
A collection of scripts for filtering annotated variant call format files
Language: Shell - Size: 80.1 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 1
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: R - Size: 10.2 MB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1
nicolo-tellini/S.cerevisiaeData
1,674 S.cerevisiae genomics data
Language: Shell - Size: 4.05 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
Joshua-Jandrell/Genome_Visualiser
Code final year dynamic genome visualizer project.
Language: Python - Size: 16.3 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
gausec/KingRailPopGen
This repository contains code related to a conservation genomics project focused on the king rail, a threatened marsh bird.
Language: Shell - Size: 12.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0
0-Ioniel-0/guppy_MR
Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.
Language: Python - Size: 665 KB - Last synced at: 6 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1
jubayer98/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 - Size: 3.91 KB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
ozankiratli/FilteringFalsePositives
This script filters false positive alleles from poolseq VCF file created with bcftools.
Language: Shell - Size: 17.6 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0
maurya-anand/liftover
Convert genomic coordinates from the Human Genome version 19 (hg19) to version 38 (hg38)
Language: Python - Size: 26.4 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
digo4/Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Language: Shell - Size: 190 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
gibsonMatt/bioneer
a tool for quickly getting the correct bcftools command
Language: Python - Size: 395 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
adrianodemarino/bcftools_merge_parallel
Merge in parallel, speeding up bcftools merge
Language: Shell - Size: 207 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
1tilly/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 - Size: 6.6 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0
biocpp/biocpp-io
BioC++ Input/Output library
Language: C++ - Size: 1.03 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 6
openb-io/ibd-pipeline
convert genotype array output into annotated IBD segments
Language: Shell - Size: 22.5 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
mnievesc/Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Language: Shell - Size: 155 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 3
sdhutchins/vcf-prepping
Scripts used on a cluster that demonstrate vcf file manipulation and preparation.
Language: Shell - Size: 3.91 KB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 0
RhettRautsaw/VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Language: Python - Size: 22.5 KB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
yenon118/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 - Size: 24.4 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
biodata-fun/course_material
This directory contains material that I've used in different courses
Size: 2.92 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
Grelot/reserveBenefit--snpsdata_analysis
Codes i wrote for the paper "genomic resources for Mediterranean fishes"
Language: Shell - Size: 2.85 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
dantaki/sv2bed
Convert SV VCFs to BED, a wrapper for bcftools query
Language: Python - Size: 13.7 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
