Giter VIP home page Giter VIP logo

pipeline's Introduction

pipeline

To run an interactive session on Itasca

qsub -I -q lab -lwalltime=8:00:00,nodes=1:ppn=6,mem=24gb

Genotype Calling

GATK4 Haplotypecaller with '--emitRefConfidence GVCF' to get reference allele depth and confidence. Results in individual gvcfs. GATK4 GenomicsDB makes a database for calling SNPs. Takes the longest, and requires all samples present. Must be redone if sample added. GATK4 GenotypeGVCFs uses database for calling SNPs on individual GVCFs.

pipeline's People

Contributors

suemcgaugh avatar

Watchers

 avatar  avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.