gatk
There are 0 repository under gatk topic.
broadinstitute / gatk
Official code repository for GATK versions 4 and up
Language:Java 1650snakemake-workflows / dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
Language:Python 234davetang / learning_vcf_file
Learning the Variant Call Format
Language:Perl 136CRG-CNAG / CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
Language:Nextflow 130GenomicsDB / GenomicsDB
High performance data storage for importing, querying and transforming variants.
Language:C++ 90gatk-workflows / gatk4-somatic-snvs-indels
This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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.
Language:WDL 76lynnlangit / TeamTeri
Bioinformatics on GCP, AWS or Azure
Language:Shell 52patidarr / ngs_pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Language:Python 45IARCbioinfo / alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
Language:Nextflow 25sib-swiss / NGS-variants-training
GitHub for the SIB courses NGS - Genome variant analysis
Language:Shell 24Sentieon / sentieon-dnaseq
Sentieon DNAseq
Language:Shell 20- Language:Scala 17
databricks / genomics-pipelines
secondary analysis pipelines parallelized with apache spark
Language:Scala 15- Language:Nextflow 12
PavlidisLab / bioluigi
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
Language:Python 9waqasuddinkhan / MACARON-GenMed-LabEx
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
Language:Python 7- Language:Python 7
AmirHoseinSafari / Genotype-collector-and-SNP-dataset-creator
Collecting Genotypes from ENA and make their SNPs
Language:Python 5- tronflow-bam-preprocessing
TRON-Bioinformatics / tronflow-bam-preprocessing
Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.
Language:Nextflow 5 dohlee / snakemake-gatk
:snake::wrench: Snakemake wrappers for GATK.
Language:Python 4mcgml / GermlineEnrichment
Variant calling pipeline for germline enrichment NGS data
Language:Shell 4programmingprincess / genome-analysis
Genome analysis pipeline that follows GATK best practices from Broad Institute
Language:Jupyter Notebook 4RhettRautsaw / VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Language:Python 4TheSergeyPixel / Diablo_G25
Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.
Language:Python 4XUKEREN / phd-pipeline
Some workflows I wrote for my phd projects
Language:Shell 4CERC-Genomic-Medicine / WEGS_pipelines
Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.
Language:Nextflow 3genomicsITER-developers / wdl
WDL-based pipelines
Language:WDL 3- Language:Perl 3
ruzhuchen / GATK4-Power
Supporting GATK4 on IBM Power architecture, including enablement, performance tuning and optimization.
Language:Dockerfile 3Vzzarr / NGS-SparkGATK
An Efficient Design of a Next Generation Sequencing pipeline with Apache Spark
Language:PostScript 3- Language:Perl 2
GeneMAP-Research / genemapngs
Workflows for whole-genome/exome sequencing data analysis
Language:Nextflow 2- Language:Shell 2
samleenz / rnaseq-variant-gatk
Variant calling + processing pipline using GATK based in Snakemake
Language:Python 2lpembleton / gatk4-when-did-dot-leave
Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.
A nextflow pipeline implementing GATK's HaplotypeCaller best practices
Language:Nextflow 1
