GitHub topics: snpeff
CDCgov/snpeffr
R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net
Language: R - Size: 80.6 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 3
brandon-hastings/manta_snpeff_parser
R code to parse Manta SV data annotated using SnpEff
Language: R - Size: 0 Bytes - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
scholl-lab/variantcentrifuge
A pipeline for filtering annotated variant call format files
Language: Python - Size: 288 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
bioinfo-chru-strasbourg/howard
Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
Language: Python - Size: 160 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 10 - Forks: 2
scholl-lab/vcf-filtering
A collection of scripts for filtering annotated variant call format files
Language: Shell - Size: 80.1 KB - Last synced at: 4 months ago - Pushed at: 4 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: 25 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1
SoloEdward/HgvsGo
HgvsGo is a program designed for analyzing "c." and "p." HGVS (Human Genome Variation Society) notations for single nucleotide variations (SNVs) and small insertions/deletions (indels) after variant calling. It serves as an alternative to tools like snpEff and VEP.
Language: C++ - Size: 2.08 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 17 - Forks: 0
tsy19900929/snpeffToMaf
Converts snpeff annotations into MAF
Language: Perl - Size: 448 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 10 - Forks: 4
COMBAT-TB/tbvcfreport
Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)
Language: Python - Size: 1.34 MB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 2 - Forks: 2
yenon118/PhenoDist
The PhenoDist pipeline is built for generating phenotype distributions for alleles in variant positions and utilizing statistical methods to test for variant position significance.
Language: Python - Size: 55.7 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
OrangePomeranian/Genomic_Analysis_Pipeline_with_Snakemake
Genomic Analysis Pipeline: Automate data preprocessing, variant calling, and annotation with Snakemake. Ensure reproducibility and reliability in genomic studies.
Language: HTML - Size: 1.08 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
yenon118/AlleleCatalog
The AlleleCatalog pipeline is built for generating Allele Catalog datasets using next-generation sequencing (NGS) based genetic data and metadata.
Language: Python - Size: 1.08 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
tdayris-perso/vcf-annotate-snpeff-snpsift 📦
Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift
Language: Python - Size: 11.4 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 2
patidarr/ngs_pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Language: Python - Size: 46.6 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 43 - Forks: 19
COMBAT-TB/vcf2neo
A tool to import SnpEff annotated files to a Neo4j Graph database
Language: Python - Size: 38.1 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2
waqasuddinkhan/MACARON-GenMed-LabEx
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
Language: Python - Size: 121 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 3
