high-coverage-wgs-gatk-genotyping-pipeline

High Coverage WGS GATK Genotyping Pipeline from UCSD Palmer Lab

https://github.com/palmer-lab-ucsd/high-coverage-wgs-gatk-genotyping-pipeline

Science Score: 67.0%

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CITATION.cff file
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Links to: zenodo.org
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Low similarity (4.6%) to scientific vocabulary

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Repository

High Coverage WGS GATK Genotyping Pipeline from UCSD Palmer Lab

Basic Info

Host: GitHub
Owner: Palmer-Lab-UCSD
License: mit
Language: Shell
Default Branch: main
Homepage:
Size: 232 KB

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Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 1

Created almost 4 years ago · Last pushed over 2 years ago

Metadata Files

Readme License Citation

README.md

alt text

Palmer Lab :test_tube: High Coverage WGS GATK Genotyping Pipeline

Overview

This github repository is to document Palmer Lab's High Coverage WGS GATK Genotyping Pipeline. We are also part of NIDA center for genetic studies of drug abuse in outbred rats.

genotyping: This folder contains the complete pipeline code that utilizes HPC's different schedulers' array jobs feature to achieve parallelization.
submissionTSCCPBS.sh: This an example of how to submit the pipeline to PBS HPC system.

Pipeline Overview

You can also visit a detalied pipeline flow here

Owner

Name: Palmer Lab
Login: Palmer-Lab-UCSD
Kind: organization
Location: United States of America

Website: https://palmerlab.org/
Repositories: 2
Profile: https://github.com/Palmer-Lab-UCSD

Behavioral Genetics of Mice, Rats and Men

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this pipeline or use data generated by this pipeline, please cite it as below."
authors:
  - family-names: Chen
    given-names: Denghui
    orcid: https://orcid.org/0000-0002-6541-3418
  - family-names: Chitre
    given-names: Apurva
  - family-names: Cheng
    given-names: Riyan
  - family-names: Peng
    given-names: Beverly
  - family-names: Polesskaya
    given-names: Oksana
  - family-names: Palmer
    given-names: Abraham
title: "Palmer Lab High Coverage WGS GATK Genotyping Pipeline"
version: 1.0.0
doi: 10.5281/zenodo.6584834
date-released: 2022-05-26
url: https://github.com/Palmer-Lab-UCSD/High-Coverage-WGS-GATK-Genotyping-Pipeline

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