Data Sciences & Data Engineering Broad Institute of Harvard and MIT http://www.broadinstitute.org/gatk

h"p://iseqtools.org/

@gatk_dev

GATK Best Practices for Variant Discovery UCLA, Los Angeles CA, USA 2-4 Mar, 2016

What/whoistheBroadIns8tute?

• SpinoffofHarvard&MIT--EricLanderandphilanthropistsEli&EdythBroad

• Usethefullpowerofgenomicstotransformtheunderstandingandtreatmentofdisease

Boston

Massachuse"s

WhereintheworldistheBroad?

Massachuse"s

Harvard

MIT

Broad

WhereintheworldistheBroad?

Massachuse"s

GATKHQ

WhereintheworldistheBroad?

DataScience&DataEngineering@Broad

Aneworganiza8onbringingtogethersoOwareengineers,computa8onalbiologists,andcompu8nginfrastructurespecialists.

Avisionthatar8culatesanadvancedcompu8nginfrastructure,setofdataandanalysisservicesleveragingmoderncloudcompu8ngparadigms.

h2ps://www.broadins>tute.org/dsde/

•  Toolkitfocusedonvariantdiscovery(SNP&indel)

•  Components:

-  Engineandinfrastructure

-  Tools(walkers)

-  AlsoaprogrammingframeworkfordevelopinggenomeanalysissoOware

GATK=GenomeAnalysisToolkit

Variantdiscovery=iden8fyvariantsinsequencingdata

RAWREADSSEQUENCEDATA

VARIANTS

GATKBestPrac8ces=completereads-to-variantsworkflows

DataPre-Processing

VariantDiscovery

CallsetRefinement

FASTQ->BAM BAM->VCF

FASTQ

SAM/BAM VCF

ExpandingecosystemofmodularBestPrac8cesworkflows

GATKdevelopmentroadmap

1.x 2.x 3.x

4.x

AlphaGATK4:cloud-friendlyandmorescalable(ApacheSpark) +extendedfunc>onality(CNVs,Picard)

h"ps://github.com/broadins4tute/gatk

=

Day1

Day2

Workshopagenda

9am–noonGermlinevariantdiscoverymethods

9am–10:30amIntroduc8ontoVariantDiscovery10:30am–noonPre-processingmethods

9am–noonSoma8cvariantdiscoverymethods

Day3

2pm–5pmHands-ontutorials

A^ernoons