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Jan2016 dnanexus giab uses andrew carroll
The document discusses using Genome in a Bottle (GIAB) data on DNAnexus cloud platform. It describes two examples: 1) Comparing different mapper and variant caller combinations using GIAB pilot genome data. Benchmarking shows BWA and GATK Haplotype Caller performed best. 2) Assessing structural variation detection in the Ashkenazi Jewish Trio, combining data from Illumina and PacBio sequencing. DNAnexus is working with GIAB to develop benchmark datasets for structural variants.
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Jan2016 dnanexus giab uses andrew carroll
- 1. The Global NetworkFor Genomic Medicine™ ® Using Genome in a Bottle Data Andrew Carroll, PhD Director of Science
- 2. ® 2 What is DNAnexus GenomicAnalysis in the Cloud. Scalable, Cost Effective, Secure, Compliant.
- 3. ® 3 What’s in theTalk • GIAB in PrecisionFDA • Datasets on DNAnexus • Example 1: Comparing mapper+variant caller combination • Example 2: Assessing structural variation in AJ-Trio
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- 10. ® 10 Public X-Ten Dataon DNAnexus
- 11. ® 11 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com BWA is used for mapping sequences against a large reference genomes, such as the human genome. It preforms very well for low divergent sequences or reads. Bowtie2 is a memory efficient tool for aligning sequencing reads to long reference sequences. It performs extremely well for sequences length between 50 bp and 1000. ISAAC, developed by Illumina, is a set of DNA sequence aligner and variant caller that uses high memory hardware to improve efficiency and accuracy. SNAP is a relatively new aligner as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. SNAP was developed by a team from the UC Berkeley AMP Lab, Microsoft, and UCSF. Mappers
- 12. ® 12 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com Atlas is a variant caller that is known differentiating between the genuine SNPs and indels from sequencing and mapping errors. It is mainly used for whole exome data. FreeBayes is a haplotype-based Bayesian genetic variant caller designed to find small polymorphisms, specifically SNPs, indels, MNPs and complex events smaller than the length of a short-read sequencing alignment. GATK Haplotype Caller is one of the most popular variant caller. It calls SNPs and Indels simultaneously using local de novo assembly and a Bayesian statistical model. ISAAC, developed by Illumina, is a set of DNA sequence aligner and variant caller that uses high memory hardware to improve efficiency and accuracy. Platypus is an efficient variant detection tool, that can detect SNPs, MNPs, short indels and replacements up to several kb. Variant Callers
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- 14. ® 14 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com Atlas Freebayes GATK ISAAC Platypus Bowrie2 0.82350 0.94507 0.95825 0.94282 0.89522 BWA 0.97194 0.94550 0.98176 0.93319 0.91955 ISAAC 0.88343 0.93066 0.96390 0.95965 0.90659 SNAP 0.86781 0.93111 0.97531 0.96337 0.91221 0.80000 0.82000 0.84000 0.86000 0.88000 0.90000 0.92000 0.94000 0.96000 0.98000 1.00000 Percentage SENSITIVITY SNPs
- 15. ® 15 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com SNPs Atlas Freebayes GATK ISAAC Platypus Bowrie2 0.99333 0.98662 0.98946 0.98716 0.98762 BWA 0.98641 0.99229 0.98857 0.93550 0.99093 ISAAC 0.99296 0.99244 0.98332 0.98800 0.99128 SNAP 0.96294 0.98893 0.97712 0.97778 0.99114 0.93000 0.94000 0.95000 0.96000 0.97000 0.98000 0.99000 1.00000Percentage SPECIFICITY
- 16. ® 16 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com SNPs Bowtie BWA ISAAC SNAP Sensitivity 0.91297 0.95039 0.92885 0.93980 Precision 0.98884 0.97874 0.98960 0.97958 0.89000 0.91000 0.93000 0.95000 0.97000 0.99000 1.01000Percentage AVERAGE Sensitivity and Specificity By Mappers
- 17. ® 17 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com Indels Atlas Freebayes GATK ISAAC Platypus Bowrie2 0.49795 0.78538 0.81924 0.81839 0.85304 BWA 0.76214 0.83467 0.79286 0.78319 0.87780 ISAAC 0.50326 0.73087 0.74374 0.78490 0.83327 SNAP 0.39509 0.71881 0.64430 0.09749 0.68149 0.00000 0.10000 0.20000 0.30000 0.40000 0.50000 0.60000 0.70000 0.80000 0.90000 1.00000 AxisTitle SENSITIVITY
- 18. ® 18 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com Indels Atlas Freebayes GATK ISAAC Platypus Bowrie2 0.78217 0.72941 0.62806 0.81787 0.65759 BWA 0.73470 0.85447 0.73998 0.69092 0.67424 ISAAC 0.62956 0.72843 0.85435 0.84755 0.66588 SNAP 0.57962 0.70933 0.64279 0.07105 0.36763 0.00000 0.10000 0.20000 0.30000 0.40000 0.50000 0.60000 0.70000 0.80000 0.90000 Percentage SPECIFICITY
- 19. ® 19 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com Bowtie BWA ISAAC SNAP CPU-hours 308.3 236 94.4 102.7 0 100 200 300 400 CPU-hour Mappers CPU-hours Atlas Freebayes GATK ISAAC Platypus CPU-hours 270.6 60.8 436.4 37.9 10.9 0 100 200 300 400 500 CPU-hour Variants Callers CPU-hours
- 20. ® 20 Benchmarking well knowbioinformatics aligners and variant callers using the Pilot Genome (NA12878) A. B. Diallo, A. Carroll, B. Hannigan, M. Kinsella, S. Ma, N. Thangaraj DNAnexus, Mountain View, CA. –email: adiallo@dnanexus.com
- 21. ® 21 Use of AJ-Trioto Understand SV
- 22. 22 Baylor College ofMedicine Characterizing large genomic variants is essential to expanding the research & clinical applications of genome sequencing. Adam English Will Salerno Narayanan Veeraraghavan Singer Ma Andrew Carroll
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- 24. 24 Development through OrthogonalTechnology
- 25. 25 Development through OrthogonalTechnology
- 26. 26 GIAB Inheritance Benhmarks DNAnexusis working actively with Genome in a Bottle to help develop high quality benchmark datasets for structural variations in the Ashkenazi Jewish Trio, applying Parliament alongside to combine Illumina and PacBio alongside other techniques.