gatk4
There are 0 repository under gatk4 topic.
nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Language:Nextflow 404gencorefacility / variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow
Language:Nextflow 52- Language:Nextflow 37
digo4 / Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Language:Shell 36biowdl / RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
Language:WDL 31ESR-NZ / human_genomics_pipeline
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Language:Python 30A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Language:WDL 24Sentieon / sentieon-dnaseq
Sentieon DNAseq
Language:Shell 22nickhir / GermlineMutationCalling
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files
Language:Python 11- Language:Shell 8
renatopuga / somatico
GATK 4 Mutect2 Somático
Language:Shell 7genome-spy / segment-model-spy
An interactive visualization tool for GATK CNV analysis. Displays modeled segments and raw read/allele counts.
Language:JavaScript 6kevin-wamae / snakemake-illumina-gatkvariant
A Snakemake workflow for variant calling using GATK4 best practices
Language:Python 5khandaud15 / RNA-Seq-Variant-Calling
Snakemake based workflow for calling Variants on RNA-Seq data in a joint calling mode
Language:Python 4SherineAwad / gatkVariantCalling
Snakemake pipeline for variant calling using GATK
Language:Python 4- Selma
elixir-no-nels / Selma
Germline Variant Calling Pipeline built in Snakemake
Language:Shell 3 jvandinter / MitoCallPipeline
A pipeline for mitochondrial mutation calling
Language:HTML 3This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)
Language:Python 3thalitacamelo / wsl2_docker_gatk
Steps that I followed setting up Windows Subsystem for Linux 2 (WSL2) and Docker to run NGS data analysis using GATK.
x-zang / tutorial-gatk4-rnaseq-germline-snps-indels
Beginner's tutorial for GATK4 workflow on variant calling from RNA-seq.
- Language:Python 2
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
Language:WDL 2tdayris-perso / wes-mapping-bwa-gatk
Map and post-process your bams for SNP calling
Language:Python 2christacaggiano / exome_processing_pipeline
simple pipeline for processing exome sequencing data using BWA and GATK4
Language:Shell 1MafaldaSFerreira / Atlherr_inversion_evol
Evolutionary genomics of chromosomal inversions in Atlantic herring
Language:R 1PavlidisLab / rnaseq-variant-pipeline
Pipeline for calling and analyzing variants from RNA-Seq data
Language:Python 1Variantes genéticas de amostras de Rattus norvegicus utilizando GATK4
Language:HTML 1zek12 / Regenotype_NGS
NGS pipeline developed with Snakemake for re-calling variants from BAM files using GATK 4.1.0.0 and weCall.
0-Ioniel-0 / guppy_MR
Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.
Language:Python 0mansikath / Variant-calling
Repository for variant calling utilizing bioinformatics tools and databases
0sebastian-gregoricchio / SPACCa
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
Language:Python 0AbhimanyuMandal / Germline-mutation
Master's Thesis Project
Language:Shell- Language:HTML
- Language:Shell
Sydney-Informatics-Hub / IndexReferenceFasta-nf
Create required reference genome index files for WGS data analysis
Language:Nextflowviolethaze74-jazzededtech / d3
Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:
Language:JavaScript
