gatk

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Here are 39 public repositories matching this topic...

broadinstitute / gatk

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Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Jul 17, 2020
Java

gatk-workflows / gatk4-somatic-snvs-indels

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This repo is archived soon, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

tumor gatk variants mutect

Updated Mar 9, 2020
wdl

CRG-CNAG / CalliNGS-NF

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GATK RNA-Seq Variant Calling in Nextflow

bioinformatics rna-seq genomics nextflow ngs gatk variant-calling

Updated Jun 15, 2020
Nextflow

davetang / learning_vcf_file

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Learning the Variant Call Format

vcf gatk vcftools bcftools vcf-files call-variants vcf-format multi-sample-vcf

Updated Jul 10, 2020
HTML

patidarr / ngs_pipeline

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Exome/Capture/RNASeq Pipeline Implementation using snakemake

snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

Updated Mar 26, 2018
Python

biopet / biopet

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Biopet docs

workflow scala pipeline gatk

Updated Aug 2, 2018
Scala

Sentieon / sentieon-dnaseq

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Sentieon DNAseq

acceleration gatk bioinformatics-pipeline variant-calling dnaseq bwa-mem dna-sequencing sentieon gatk4 genomics-data

Updated Feb 6, 2020
Shell

wtsi-hgi / gatk-cwl-generator

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Generates CWL files from the GATK documentation

gatk cwl

Updated Aug 1, 2018
Python

IARCbioinfo / alignment-nf

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Whole Exome/Whole Genome Sequencing alignment pipeline

nextflow ngs gatk alignment bwa whole-exome-sequencing whole-genome-sequencing

Updated Jul 13, 2020
Nextflow

waqasuddinkhan / MACARON-GenMed-LabEx

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Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

github python vcf gatk variants snp annotator macaron snv annotation-framework snpeff snv-annotation codon snpcluster pcsnv

Updated May 18, 2020
Python

PavlidisLab / bioluigi

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Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

bioinformatics slurm gatk vcfanno bcftools luigi-task ensembl-vep

Updated Jun 25, 2020
Python

dohlee / snakemake-gatk

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🐍

🔧 Snakemake wrappers for GATK.

snakemake reproducible-research gatk bioinformatics-pipeline bioinformatics-analysis snakemake-workflows

Updated Sep 21, 2018
Python

mcgml / GermlineEnrichment

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Variant calling pipeline for germline enrichment NGS data

bioinformatics ngs gatk diagnostics variant-calling

Updated Feb 26, 2018
Shell

Vzzarr / NGS-SparkGATK

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An Efficient Design of a Next Generation Sequencing pipeline with Apache Spark

docker spark hadoop docker-swarm ngs gatk hdfs ngs-pipeline

Updated Apr 6, 2018
PostScript

samleenz / rnaseq-variant-gatk

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Variant calling + processing pipline using GATK based in Snakemake

rna-seq snakemake gatk snp-genotyping

Updated May 31, 2018
Python

davetang / tang_sd_2015

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gatk

Updated Feb 10, 2017
Perl

genomicsITER-developers / wdl

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WDL-based pipelines

workflow bioinformatics pipeline gatk wdl whole-exome-sequencing whole-genome-sequencing

Updated Nov 9, 2018
wdl

ruzhuchen / GATK4-Power

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Supporting GATK4 on IBM Power architecture, including enablement, performance tuning and optimization.

performance optimization gatk ibm power9

Updated Jul 2, 2020
Dockerfile

CNoune / IMG_pipelines

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Bash and Python pipelines and scripts from the Invertebrates & Microbiology Group at the Queensland University of Technology to help make data analysis easy.

python bioinformatics pipeline analysis gatk qut invertebrates