Sept2016 sv pb_honey

1. GIAB SV Data Jamboree @ NIST
PBHoney Spots Update
Will Salerno
9.15.2016
PBSuite
http://sourceforge.net/projects/pb-jelly/

2. Honey Spots
● Honey Spots is the “indel” caller
for Long-Read SV detection
○ Tails is “split read”
● Designed for smaller SVs
○ 50 bp to 2 Kbp
● Two components
○ SpotCaller: Discover
putative SVs
○ ConsensusCaller: Evaluate
SVs
Align Reads &
Create Error
Channels
Process Signal &
Create “Spots”
Identify Alt Reads
& Create
Consensus
Sequence
Remap Consensus
& Call SV

3. Honey Spots Update
● Performance Optimizations
○ NA12878 (41x) 2 days to 6
hours
● Less restrictive filtering
○ More sensitive calling
● “Tails” can contribute to Spots
signal
Align Reads &
Create Error
Channels
Process Signal &
Create “Spots”
Identify Alt Reads
& Create
Consensus
Sequence
Remap Consensus
& Report All Spots
Tails Calls <10
Kbp

4. Existing Data Sets
AJ Proband AJ Mother AJ Father NA12878 HS1011
Coverage 45x 19x 21x 41x 23x
● Eight short-read SV detection methods
● PBHoney (old version)
● 10x PacBio, 48x Short-Read, BioNano, aCGH

5. Honey Spots Performance
Sample
SVTyp
e SizeDist Count
TruthSet
Calls
TruthSet
Recovered
Recovery
Rate
HS1011
INS
(50, 100) 6,459 113 74 65.49%
(101, 500) 6,277 2,850 2,383 83.61%
(501, 1000) 673 305 241 79.02%
(1000, 2000) 103 259 192 74.13%
DEL
(50, 100) 5,405 25 19 76.00%
(101, 500) 4,067 3,159 2,582 81.73%
(501, 1000) 600 226 170 75.22%
(1000, 2000) 536 46 15 32.61%
NA12878
INS
(50, 100) 8,833 . . .
(101, 500) 8,460 . . .
(501, 1000) 676 . . .
(1000, 2000) 66 . . .
DEL
(50, 100) 5,010 2 2 100.00%
(101, 500) 3,930 1,484 1,446 97.44%
(501, 1000) 509 201 182 90.55%
(1000, 2000) 466 197 185 93.91%

6. AJ Trio Deletions: Trio Discovery
Remove loci with
any sample
represented
more than once
Do discovery
in Trio
Filter Proband
to
altZMWs >= 10
Merge Trio
With
50bp Bookends
Distance
Force Call
Missing in
Parents
Discovery
Filter
Proband
altZMWs
>=10 50bp Merge
Single
Sample
Filter
Present in
Proband
and
Parent(s)
Missing in
Parents
Discovery
but Forced
Total
Proband
with Parent
Support
Proband 10,753 8,137 7,785 7,305 6,175 886 7,061
Father 7,994 . 7,727 7,300 4,784 663 5,447
Mother 7,448 . 7,217 6,813 4,636 651 5,287
Total 26,195 23,579 11,896 11,369 6,175 886 7,061

7. Honey Force Calling
Candidate Regions
Identify Matching
Spots Reads Near
Region
Output Evidence
Identify Matching
Tails Reads Near
Region
Identify ‘Reference’
Supporting Reads
Spanning Region
● A Candidate Region is an SV’s location, type, size.
● Reads are fetched within Region ±BUFFER.
● Matching Reads are those having variant of the same type within ±SIZE and ±DISTANCE.
● Reference supporting Reads span Region and show no variant evidence.
● Looking for a minimum of one read.

8. AJ Trio Dels: Proband Discovery, Parent Force Calling
Do discovery
in Proband
Filter Proband
to
altZMWs >= 10
Force in Parents
Discovery
Filter Proband
altZMWs
>= 10
Forced in
Father
Forced in
Mother
Forced in
Parent(s)
Proband 10,753 8,137 6,268 6,206 7,565

9. AJ Trio Insertions: Trio Discovery
Discovery
Filter
Proband
altZMWs
>=10 50bp Merge
Single
Sample
Filter
Present in
Proband
and
Parent(s)
Missing in
Parents
Discovery
but Forced
Total
Proband
with Parent
Support
Proband 24,585 13,134 12,324 11,317 7,266 2,986 10,252
Father 11,758 . 11,236 10,303 5,632 2,322 7,954
Mother 10,633 . 10,146 9,253 5,344 2,308 7,652
Total 26,195 35,525 20,227 19,051 7,266 2,986 10,252
Remove loci with
any sample
represented
more than once
Do discovery
in Trio
Filter Proband
to
altZMWs >= 10
Merge Trio
With
50bp Bookends
Distance
Force Call
Missing in
Parents

10. AJ Trio Ins: Proband Discovery, Parents Force Calling
Discovery
Filter Proband
altZMWs
>= 10
Forced in
Father
Forced in
Mother
Forced in
Parent(s)
Proband 24,585 13,134 10,245 10,139 11,839
Do discovery
in Proband
Filter Proband
to
altZMWs >= 10
Force in Parents

11. Next-Gen Sequencing Informatics Group @ HGSC
● Bioinformatics Core for the Human Genome Sequencing Center
● Primary and Secondary Analysis for Production Pipelines
○ Illumina Fleet (X Ten, 2000/2500), PacBio (RS II and Sequel)
○ Research and CAP/CLIA
○ WGS, WES, Custom Capture, Clinical Panels
● Structural Variation
● Annotation
● Hadoop Data Warehouse
● EMR/EHR Integration
● 11 Members and Growing!
CHARGE