gatk | Topic | Ecosyste.ms: Repos

Topic: "gatk"

broadinstitute/gatk

Official code repository for GATK versions 4 and up

Language: Java - Size: 463 MB - Last synced at: about 19 hours ago - Pushed at: 1 day ago - Stars: 1,847 - Forks: 614

snakemake-workflows/dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

Language: Python - Size: 9.14 MB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 250 - Forks: 145

davetang/learning_vcf_file

Learning the Variant Call Format

Language: Perl - Size: 42.7 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 144 - Forks: 40

CRG-CNAG/CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Language: Nextflow - Size: 29 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 133 - Forks: 53

GenomicsDB/GenomicsDB

High performance data storage for importing, querying and transforming variants.

Language: C++ - Size: 65.9 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 98 - Forks: 16

gatk-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This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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 - Size: 151 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 76 - Forks: 42

lynnlangit/TeamTeri

Bioinformatics on GCP, AWS or Azure

Language: Shell - Size: 135 MB - Last synced at: 8 days ago - Pushed at: 14 days ago - Stars: 58 - Forks: 17

patidarr/ngs_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Language: Python - Size: 46.6 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 43 - Forks: 19

IARCbioinfo/alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

Language: Nextflow - Size: 3.73 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 26 - Forks: 12

sib-swiss/NGS-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

Language: Shell - Size: 69.4 MB - Last synced at: 1 day ago - Pushed at: 9 months ago - Stars: 25 - Forks: 9

Sentieon/sentieon-dnaseq 📦

Sentieon DNAseq

Language: Shell - Size: 60.5 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 12

biopet/biopet

Biopet docs

Language: Scala - Size: 11.5 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 17 - Forks: 3

databricks/genomics-pipelines

secondary analysis pipelines parallelized with apache spark

Language: Scala - Size: 14 MB - Last synced at: 9 days ago - Pushed at: over 3 years ago - Stars: 16 - Forks: 12

isugifNF/GATK-flow

Nextflow implementation of the GATK HaplotypeCaller pipeline

Language: Nextflow - Size: 2.34 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 13 - Forks: 2

PavlidisLab/bioluigi

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Language: Python - Size: 121 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 9 - Forks: 0

waqasuddinkhan/MACARON-GenMed-LabEx

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

Language: Python - Size: 121 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 3

wtsi-hgi/gatk-cwl-generator

Generates CWL files from the GATK documentation

Language: Python - Size: 42.5 MB - Last synced at: 2 months ago - Pushed at: about 7 years ago - Stars: 7 - Forks: 1

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 - Size: 8.56 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 0

AmirHoseinSafari/Genotype-collector-and-SNP-dataset-creator

Collecting Genotypes from ENA and make their SNPs

Language: Python - Size: 40 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 0

Nucleomics-VIB/admin-tools

sysadmin tasks made easier

Language: Shell - Size: 221 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

mcgml/GermlineEnrichment

Variant calling pipeline for germline enrichment NGS data

Language: Shell - Size: 8.69 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 3

dohlee/snakemake-gatk

:snake::wrench: Snakemake wrappers for GATK.

Language: Python - Size: 49.8 KB - Last synced at: 16 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 4

esohkevin/ei-ngs

Workflows for whole-genome/exome sequencing data analysis

Language: Nextflow - Size: 684 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 3 - Forks: 1

CERC-Genomic-Medicine/WEGS_pipelines

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

Language: Nextflow - Size: 4.07 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

genomicsITER-developers/wdl

WDL-based pipelines

Language: wdl - Size: 494 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 0

ruzhuchen/GATK4-Power

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

Language: Dockerfile - Size: 48.8 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 3

programmingprincess/genome-analysis

Genome analysis pipeline that follows GATK best practices from Broad Institute

Language: Jupyter Notebook - Size: 1.89 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

Vzzarr/NGS-SparkGATK

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

Language: PostScript - Size: 28.1 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1

plantinformatics/shortbread2

Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.

Language: Perl - Size: 819 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 1

georgiesamaha/fq2vcf

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

Language: Shell - Size: 54.7 KB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

TheSergeyPixel/Diablo_G25

Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.

Language: Python - Size: 15.4 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

modupeore/VAP

VAP : For Reference mapping and Variant detection.

Language: Perl - Size: 21.5 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 4

colbyford/msgen

msgen: R functions for interfacing with the Microsoft Genomics service on Azure.

Language: R - Size: 1.19 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

labbcb/hpexome

An automated tool for processing whole-exome sequencing data

Language: Python - Size: 41.6 MB - Last synced at: 22 days ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 5

samleenz/rnaseq-variant-gatk 📦

Variant calling + processing pipline using GATK based in Snakemake

Language: Python - Size: 61.5 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

davetang/tang_sd_2015

Language: Perl - Size: 18.6 KB - Last synced at: 6 days ago - Pushed at: over 8 years ago - Stars: 2 - Forks: 2

TRON-Bioinformatics/tronflow-haplotype-caller

A nextflow pipeline implementing GATK's HaplotypeCaller best practices

Language: Nextflow - Size: 9.14 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

lpembleton/gatk4-when-did-dot-leave

Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.

Size: 76.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

laura-budurlean/GATK-WGS-Pipeline

GATK WGS workflow

Language: Shell - Size: 10.7 KB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

oicr-gsi/gatk3

Language: Java - Size: 703 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

lvn3668/gatkparser

Python package to parse GATK Output and extract summary statistics at mbq 0,10,20,30 and variant evaluation metrics

Language: Python - Size: 15.3 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

AlexanderKononov/pipeline_cloneHD

Toolbox for work with CloneHD application

Language: Shell - Size: 13.7 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

christacaggiano/exome_processing_pipeline

simple pipeline for processing exome sequencing data using BWA and GATK4

Language: Shell - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

BU-ISCIII/exome_pipeline 📦

Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

Language: Shell - Size: 199 MB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

rbpisupati/nf-haplocaller

Nextflow pipeline for GATK best practices (HaplotypeCaller)

Language: Nextflow - Size: 17.6 KB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 2

zek12/NGS_scripts

Language: Shell - Size: 1.19 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

RRafiee/GenomeAnalysisToolkit

Genome Analysis Toolkit

Language: R - Size: 45.9 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

svsuresh/ngs_scripts

This repository contains bash shell scripts

Language: R - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

drveera/exomepipe

A pipeline for variant calling of Exome using GATK best practice workflow

Language: Makefile - Size: 17.6 KB - Last synced at: over 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

HaoKuo/NGS-pipeline

GATK and VARSCAN analysis pipeline

Language: Python - Size: 18.6 KB - Last synced at: over 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

afreeorange/autozygosity

A public, web-based homozygosity mapping tool

Language: Python - Size: 3.51 MB - Last synced at: over 1 year ago - Pushed at: over 11 years ago - Stars: 1 - Forks: 1

sebastian-gregoricchio/SPACCa

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

Language: Python - Size: 4.74 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

alexliyihao/EFIGA_WGS

Implementation of WGS genotyping pipeline for EFIGA FBS FAMILY dataset

Language: Shell - Size: 104 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

mmterpstra/molgenis-c5-TumorNormal

Language: Shell - Size: 12.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

GiatrasKon/Chromosome11-VariantCalling-GATK

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

Language: R - Size: 10.2 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

nunososorio/Pfalciparum-ReducedACT-Susceptibility

This repository contains data and code for our analysis of the genome of a Plasmodium falciparum strain with reduced susceptibility to Artemisinin-Based Combination Therapy (ACT) drugs. We performed whole-genome sequencing of the HSOG3 clinical isolate and compared it with a large dataset of global P. falciparum samples.

Language: Python - Size: 34.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

anita-brzoza/university_projects

The repository contain directories of projects done during the bioinformatics degree program

Language: HTML - Size: 894 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

lajd/reads2variants

Convert NGS reads to analysis ready variants with GATK's ReadsPipelineSpark

Language: Python - Size: 263 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

RhettRautsaw/VariantCaller

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

Language: Python - Size: 22.5 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

beroukhim-lab/GATK_CN_CWL

Implementation of the GATK copy number pipeline in CWL (ported from WDL)

Language: Common Workflow Language - Size: 91.8 KB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

SherineAwad/RNASeqVariantCalling

GATK variant calling for RNASeq

Language: Python - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ahalfpen727/VariantAnalysisScripts

Several variant analysis workflows for different types of sequencing data

Language: R - Size: 12.5 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

ruizhideng/wgs_pipeline

Language: Shell - Size: 5.72 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

zek12/dockerized_gatk_pipeline

Dockerized version of the GATK 3.7 best practises pipeline for whole genomes.

Language: Shell - Size: 14.6 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

datasnakes/pyVariant 📦

A pipeline to call variants for RNASeq implemented with python.

Size: 0 Bytes - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0