Aug2015 analysis team 13 carroll dnanexus parliament talk

1. Andrew Carroll, DNAnexus
Assessing Structural Variation
in the SV trio with Parliament
1

2. 2
Baylor College of Medicine
Characterizing large genomic variants is essential to expanding the
research & clinical applications of genome sequencing.
Adam
English
Will
Salerno
Narayanan
Veeraraghavan
Singer
Ma

3. 3
Characterization of High Quality Reference

4. 4
Parliament Pipeline

5. 5
Work Done on AJ Tri
• Mapping to generate representative sets of 30X
Illumina genomes and PacBio genomes
• Calling with Individual
short-read callers
– Lumpy, Breakdancer,
Pindel, Delly
• Assessment of concordance
with Mendelian inheritance on
short-read callers individually
• Combined calling with Parliament (forcing
genotype calls on all child sites) and assessment
Samantha
Zarate

6. 6
(Crude) Assessment of Individual Callers by
Inheritance
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
70.00%
80.00%
90.00%
100.00%
Concordance of Individual Callers with Mendelian Inheritance

7. 7
Parliament Output – Force Calling
21 18612385 18613634 DEL
True[|21:18612385-18613634(DEL)1300] True[|21:18612385-18613634(DEL)1311]
0/1 HYBRID_ASSEMBLY,PACBIO
21 18612385 18613634 DEL
True[|] True[|]
0/0 NONE
HG002
HG003
21 18612385 18613634 DEL
False[|21:18612385-18613634(DEL)1310] False[|21:18612385-18613634(DEL)1033]
1/1 HYBRID_ASSEMBLY,PACBIO
HG004

8. 8
Parliament Concordance (Crude)
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
70.00%
80.00%
90.00%
100.00%
Illumina Assembly Pacbio
Concordance of Parliament with (Crude) Mendelian Inheritance

9. 9
Parliament Concordance (Full)
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
70.00%
80.00%
90.00%
100.00%
Illumina Assembly Pacbio
Concordance with Mendelian Inheritance (and correctly genotyped)

10. 10
Future Work
• Release a full callset for Parliament on AJ Trio
• Force calling and evaluation of regions
nominated by other methods (can take BED or
VCF)
• Titration curve of Illumina + Pacbio
• Use of Parliament-validated calls as TP, failed
validation as FP set, application of SVClassify
from Hemang Parikh + ML
• Swapping of local assembler behind Parliament

11. 11
THANKS
Adam
English
Will
Salerno
Narayanan
Veeraraghavan
Singer
Ma
Justin and Genome in a Bottle
for Organizing
Samantha
Zarate