Oleksiy Karpenko, Neil J. Bahroos Galaxy Community Conference Chicago

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Presentation transcript:

Galaxy Pipeline for Faster Whole Genome Genotype Calling on the GeneTitan Platform Oleksiy Karpenko, Neil J. Bahroos Galaxy Community Conference Chicago July 26, 2012

Overview What is Affymetrix GeneTitan? Axiom® Genome-Wide Population-Optimized Human Arrays Affymetrix Power Tools (APT) vs Affymetrix Genotyping Console APT in Galaxy at UIC Galaxy workflow for Axiom® arrays Future work

Affymetrix GeneTitan Automated high-throughput solution for monitoring gene expression and genome-wide SNP genotyping 16-, 24- and 96-format array plates On campus at RRC Core Genomics Facility, College of Medicine West (CMW), Room A-301

AXIOM® GENOME-WIDE POPULATION-OPTIMIZED HUMAN ARRAYS One Axiom Genome-Wide PanAFR Plate for 96 samples ~700K SNPs per plate One Axiom GW (~2.1M) PanAFR Array Set is a set of 3 plates Also available CEU (European), ASI (Asian), CHB (Chinese Beijing), and custom myDesign plates

POWER TOOLS VS GENOTYPING CONSOLE Affymetrix Power Tools Genotyping Console

AFFYMETRIX POWER TOOLS IN GALAXY apt-geno-qc for quality control apt-probeset-genotype for genotype calling Write calls in plink format SNP metrics

MINOR CUSTOMIZATIONS Registered ".CEL.TAR" file formats for batch uploads Modified Galaxy upload tool for better handling custom binary files Registered APT ".calls.txt", ".report.txt", "snp-posteriors.txt“ file formats Registered PLINK formats ".tped", "tmap"

#1. Upload a tarball of .CEL files

#2. Perform QC for each .CEL file

#3, #4. Filter .CEL files above 0.82 DQC #2. Perform QC for each .CEL file

#5. First run of genotyping

#6, #7. Filter .CEL files above 97% Call Rate #2. Perform QC for each .CEL file

#8. Second run of genotyping

#9. Calculate different SNP metrics

#10. Upload phenotypes

#11. Output genotypes in PLINK format

Future work Integrate a few more Affymetrix Power Tools into Galaxy Publish the APT tools in Galaxy Tool Shed Better support for binary/compressed data files Publish the APT genotyping workflow

Acknowledgements Research Resources Center and Center for Clinical and Translational Science at UIC Dr. Damir Herman, Affymetrix Morris Chukhman, Tommie Jackson, and the team at the Center for Research Informatics at UIC Dr. Rick Kittles, UIC Institute of Human Genetics Dr. Zarema Arbieva, UIC Core Genomics Facility

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