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

  nextflowworkflowpipelinebioinformaticsgenomicscancernext-generation-sequencingcondareproducible-researchcontainersgermlinesomaticvariant-callingnf-coregatk4annotationwhole-genome-sequencingwhole-exome-sequencingpre-processingtarget-panels
  Language:Nextflow 333

• gencorefacility / variant-calling-pipeline-gatk4

  Variant Calling Pipeline Using GATK4 and Nextflow

  bioinformaticsbioinformatics-pipelinegatk4genomicsnextflowvariant-calling
  Language:Nextflow 47

• biowdl / RNA-seq

  A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

  pipelinemultisamplerna-seqwdlgatk4gatk-bestpractices
  Language:WDL 30

• nf-core / rnavar

  gatk4 RNA variant calling pipeline

  gatk4variant-callingrnaseqrnaworflowpipelinenextflownf-coreworkflow
  Language:Nextflow 28

• ESR-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.

  pipelinegenomicsnvidia-clara-parabricksnvidia-gpusnakemake-pipelinegatk4gatk-bestpracticesilluminaexome-pipelinecohort-analysis
  Language:Python 27

• biowdl / germline-DNA

  A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

  pipelinevariantcallingmultisamplewdlgatk-bestpracticesgatk4germline-variantssomatic-variantsstructural-variation
  Language:WDL 23

• Sentieon / sentieon-dnaseq

  Sentieon DNAseq

  dna-sequencingvariant-callingbioinformatics-pipelinesentieondnaseqgenomics-databwa-memaccelerationgatkgatk4
  Language:Shell 19

• digo4 / Clinical-Genomics

  Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

  bcftoolsbowtie2bwa-memcutadaptfastpfastqcfreebayesgatk-bestpracticesgatk-cnvgatk-joint-variant-calling-workflowgatk4gatk4-haplotypecallerpicardsamtoolstrimgaloretrimmomaticvarscan
  Language:Shell 13

• nickhir / GermlineMutationCalling

  An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

  bioinformatics-pipelinesnakemakegatk4gatk-bestpractices
  Language:Python 12

• renatopuga / somatico

  GATK 4 Mutect2 Somático

  gatk4mutect2ponsomatic-variantsgitpodcolab-notebookhg19normaltumorvep
  Language:Shell 7

• Vicellken / Whole_exome_sequence

  shellscriptpythonwhole-exome-sequencinggatk4pipeline
  Language:Shell 7

• genome-spy / segment-model-spy

  An interactive visualization tool for GATK CNV analysis. Displays modeled segments and raw read/allele counts.

  gatk-cnvgatk4visualization
  Language:JavaScript 6

• kevin-wamae / snakemake-illuminaVarGATK

  A Snakemake workflow for variant calling using GATK4 best practices

  bioinformaticsgatk4ngsvariant-annotationsvariant-calling
  Language:Python 4

• khandaud15 / RNA-Seq-Variant-Calling

  Snakemake based workflow for calling Variants on RNA-Seq data in a joint calling mode

  rna-seqpythonsnakemakevariant-callinggatk4picard
  Language:Python 4

• SherineAwad / gatkVariantCalling

  Snakemake pipeline for variant calling using GATK

  gatk4pipelinesnakemakevariant-calling
  Language:Python 4
• Selma

  elixir-no-nels / Selma

  Germline Variant Calling Pipeline built in Snakemake

  containerizedgatk4germline-variant-callingscatter-gathersingularitysnakemake
  Language:Shell 3

• jvandinter / MitoCallPipeline

  A pipeline for mitochondrial mutation calling

  geneticsmitochondrial-variantsmitochondriagatk4somatic-variantsrwdl-workflow
  Language:HTML 3

• SherineAwad / SomaticMutations

  This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)

  gatk4mutationsmutect2snakemakesomatic
  Language:Python 3

• x-zang / tutorial-gatk4-rnaseq-germline-snps-indels

  Beginner's tutorial for GATK4 workflow on variant calling from RNA-seq.

  rna-seqvariant-callinggatk4
  3

• AntoineHo / runGATK

  Small GATK alignment and variant calling pipeline using python

  gatk4parallelpython-wrappervariant-callingalignmentbwabwa-mempipelinevcfgenomicspopulationpopulation-genomics
  Language:Python 2

• biowdl / gatk-variantcalling

  A pipeline that calls variants on a group of BAM files. Category:Multi-Sample

  bioinformaticsworkflowsworkflowgatk4gatk-bestpracticesvariant-calling
  Language:WDL 2

• tdayris-perso / wes-mapping-bwa-gatk

  Map and post-process your bams for SNP calling

  snakemake-workflowsbioinformatics-pipelinereproducible-researchwhole-exome-sequencingbwagatk4fastqcmultiqc
  Language:Python 2

• thalitacamelo / wsl2_docker_gatk

  Steps that I followed setting up Windows Subsystem for Linux 2 (WSL2) and Docker to run NGS data analysis using GATK.

  wsl2gatk4docker
  2

• christacaggiano / exome_processing_pipeline

  simple pipeline for processing exome sequencing data using BWA and GATK4

  exomegatkgatk4
  Language:Shell 1

• PavlidisLab / rnaseq-variant-pipeline

  Pipeline for calling and analyzing variants from RNA-Seq data

  gatk4picardstarrnaseq-pipelinevariant-callingluigi-workflowsrnaseq
  Language:Python 1

• renatopuga / exoma-de-rato

  Variantes genéticas de amostras de Rattus norvegicus utilizando GATK4

  bioinformaticsexomerattus-norvegicusbwagatk4vepannotationseducation
  Language:HTML 1

• zek12 / Regenotype_NGS

  NGS pipeline developed with Snakemake for re-calling variants from BAM files using GATK 4.1.0.0 and weCall.

  snakemakengsgatk4
  1

• 0-Ioniel-0 / guppy_MR

  Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.

  bambcftoolsdenovogatk4gvcfmutation-ratepythonsamtoolsvcf
  Language:Python 0
• gi-proj-CNNScoreVariants

  nikolapeja6 / gi-proj-CNNScoreVariants

  School project for the Computational Genomics (2018/2019) course, which is a part of the Master studies at the School of Electrical Engineering, University of Belgrade.

  genomicscancer-genomics-cloudcommon-workflow-languagecwldockergatk4school-projectrabixcgc
  Language:Common Workflow Language 0

• sebastian-gregoricchio / SPACCa

  Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

  chip-seqchip-seq-analysischip-seq-callerschip-seq-datachip-seq-peakschipseqcopynumbergatkgatk4macsmacs2mutationmutation-analysismutationsnormalizationsomatic-indelssomatic-mutationssomatic-variantsomatic-variants
  Language:Python 0

• yenon118 / snakyVC

  The snakyVC pipeline is designed for efficiently and parallelly executing variant calling on next-generation sequencing (NGS) whole-genome datasets.

  snakemakedna-sequencingbwagatk4python3
  Language:Python 0

• alperyilmaz / conda-snakemake-gatk

  snakemake pipeline for gatk running on binder

  snakemakepython-workflowgatk4bioconda
  Language:HTML

• j23414 / atlas_gatk4

  Testing gatk4 module on Atlas HPC

  gatk4
  Language:HTML

• renatopuga / rnaseq-callvariants

  RNASeq and Call Variants

  rnaseqngscall-variantsedgergatk4starrsem
  Language:Shell

• Sydney-Informatics-Hub / IndexReferenceFasta-nf

  Create required reference genome index files for WGS data analysis

  bioinformaticsbwadockerfastagatk4genomegenomicsindexnextflowpipelinereference-genomesamtoolssingularityworkflow
  Language:Nextflow

• violethaze74-jazzededtech / d3

  Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

  nginx-proxynodejsnpm-packagedebunitygenomicscloudmangalaxy-adminubuntu-packagessnapcraftsnapdcanonicalcloudcloud-initnextcloud-serverphpmyadminugenegatk4picardpromethease
  Language:JavaScript