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Ensembl Vep ⭐ 410

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Vcf2maf ⭐ 305

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Vardict ⭐ 182

Vardictjava ⭐ 125

VarDict Java port

Learning_vcf_file ⭐ 122

Learning the Variant Call Format

Vep_plugins ⭐ 121

Plugins for the Ensembl Variant Effect Predictor (VEP)

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Mutation Identification Pipeline. Read the latest documentation:

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Variant Filter ⭐ 25

A false-positive filter for variants called from massively parallel sequencing

Gbs Snp Crop ⭐ 24

GBS SNP Calling Reference Optional Pipeline

Prioritize structural variants based on CADD scores

X11 bitmap terminal fonts, and one specifically for crawl

Garfield Ngs ⭐ 16

GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS

Malware Phylogeny ⭐ 14

malware phylogeny for WSO web shell, Shellbot IRC bot and algorithm

Variantdb_challenge ⭐ 14

Finding a scalable alternative to the VCF File for genomics analysis

Computational Genome Analysis ⭐ 11

Website for Computational Exome and Genome Analysis

Microhaplot ⭐ 11

microhaplotype visualizer and analyzer

Heliotrope ⭐ 10

Annotation Pipeline ⭐ 10

Funseq2_dc ⭐ 10

a modified version of FunSeq2 using new data context

Bioscripts ⭐ 9

Scripts for bioinformatics data processing and analysis

FLT3 ITD detection (ITDseek) and simulation (ITDsim)

Vafcorrect ⭐ 8

Calculates the Variant Allele Fraction of variants in VCF files

Somaticwrapper ⭐ 8

Detect somatic variants from tumor and normal WGS/WXS data

A wrapper for calling small variants from human germline high-coverage single-sample Illumina data

A scalable variant calling and benchmarking framework supporting both short and long reads.

Vargenius ⭐ 7

VarGenius is a software for variants discovery and annotation. It allows efficient management of folder data and jobs submission into a PBS cluster. All the variants will be inserted into a PostgreSQL database that can be used for downstream analyses. It is written with PERL, R and HTML languages and uses Picard, Samtools, BWA, GATK and Annovar!

Impact Sv ⭐ 7

Detection of Structural Variants Using Delly and Annotation using dRanger

A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

Variant Assurance Pipeline

Explore and filter structural variant calls from Lumpy and Delly VCF files

2019genomicsepidemiologyworkshop ⭐ 6

2019 Genomics Epidemiology Workshop at Academia Sinica

VAriant Mapping and Prediction of antimicrobial resistance

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