variant-calling
There are 267 repositories under variant-calling topic.
gencorefacility/variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow
HKU-BAL/ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
karel-brinda/ococo
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
Clinical-Genomics/BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
NVIDIA/VariantWorks
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
kevlar-dev/kevlar
Reference-free variant discovery in large eukaryotic genomes
nf-core/deepvariant
Please consider using/contributing to https://github.com/nf-core/sarek
brentp/indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
nf-core/rnavar
gatk4 RNA variant calling pipeline
kehrlab/PopDel
Population-wide Deletion Calling
PacificBiosciences/sawfish
Structural variant discovery and genotyping from mapped PacBio HiFi data
adrianodemarino/Imputation_beagle_tutorial
Imputation-beagle-tutorial
gear-genomics/indigo
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
oliverSI/GATK4_Best_Practice
GATK4 Best Practice Nextflow Pipeline
sib-swiss/NGS-variants-training
GitHub for the SIB courses NGS - Genome variant analysis
SUwonglab/arcsv
Complex structural variant detection from WGS data
aryarm/varCA
Use an ensemble of variant callers to call variants from ATAC-seq data
Sentieon/sentieon-dnaseq
Sentieon DNAseq
IKIM-Essen/uncovar
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
sanjaynagi/rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
TimD1/nPoRe
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
HKU-BAL/Clair3-RNA
Clair3-RNA - a long-read small variant caller for RNA sequencing data
nf-core/exoseq
Please consider using/contributing to https://github.com/nf-core/sarek
tjiangHIT/rMETL
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
HKU-BAL/Clair3-Trio
Clair3-Trio: variant calling in trio using Nanopore long-reads
NBISweden/workshop-ngsintro
Workshop • Intro to Bioinformatics using NGS data • 5 days
nf-core/vipr
Assembly and intrahost / low-frequency variant calling for viral samples
pdimens/harpy
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Sydney-Informatics-Hub/Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
nshomron/hoobari
Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.
collaborativebioinformatics/Sniphles
Sniphles is a read-based phasing approach for phased variant calling of structural variants.
Sentieon/sentieon-dnascope-ml
Sentieon DNAscope + Machine Learning Model
tobiasrausch/nRex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling