Aug2015 analysis team 07 fritz and schatz pac_bio sv
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Transcript of Aug2015 analysis team 07 fritz and schatz pac_bio sv
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Methods for improved SV detection and interpretation
Fritz J SedlazeckSchatz group @ CSHL
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Breast Cancer
75x PacBio coverage (50x >10kbp)
Nattestad et al, In preparation
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Breast Cancer PipelinePacBio Sequencing
Alignment with BWA-MEM
Copy number analysis
SV-calling with Lumpy
Graphical genome threading analysis
Assembly with Falcon on DNAnexus
Alignment with MUMmer (nucmer)
Call variants between
consecutive alignments
Call variants within alignments
IsoSeq transcriptome
analysis
...
Detailed analysis of Her2
amplifications
Validation using PCR.
Illumina sequencing
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What we learnedIllumina:
– Nested SV are hard to detect – Problems with repetitive regions
PacBio:– Tools are not yet as accurate– Erroneous alignments hide SV
Assembly vs. mapping– Detection of more SV over assembly– Assembly misses low frequent SVs– Comparing the assembly to the genome is still challenging
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What we can offer
• Improve alignments:– NextGenMap-LR*
• Improve SV detection:– Survivor (illumina)– Sniffles (PacBio)*– Assembly guided detection (PacBio)
• Interpretation of the SV:– SplitThreader*
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NextGenMap-LR
• Novel algorithms to make mapper aware of SV region
– Builds on very fast and robust NextGenMap algorithms (Sedlazeck et al. Bioinformatics. 2013)
• Major benefits from pairwise alignment with improved scoring functions– Accounts for long (SV) and smaller (error) gaps – SVs are better represented, cleaner breakpoints
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NextGenMap-LRBWA-MEM NextGenMap-LR
Very stable deletion calls
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NextGenMap-LRBWA-MEM NextGenMap-LR
Very stable insertion call
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Sniffles
• Predicts: deletion, duplication, insertion, inversion, translocations and nested SV
• Designed to overcome the problems of current SV callers.
• Scans for erroneous regions in the alignment and predict if they overlap.
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Sniffles
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Sniffles (Inversion)
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SplitThreader
• Graph based tool that uses SV calls.
• Identifies the most likely paths that forms the chromosomes.
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50 Mb
Chr 8
PacBio
PacBio
Her2
Chr 17
RARA
PKIA
GSDMB
TATDN1
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Cancer lesion reconstruction from genomic threads
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How we could contribute
1. Calling SV using PacBio
2. Calling SV using Illumina
3. Interpretation of Structural Variants
Thanks to:Schatz group + McCombie group + Hicks group + OICR + PacBio + DNAnexus