Linked-Reads for Improved Genomics
Sarah Garcia, PhD
Wednesday, February 1, 2017
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Chapters
Introduction
The Search for Causative Variation pt.1
The Search for Causative Variation pt.2
The Search for Causative Variation pt.3
Linked-Reads
Partitioning to Linked Reads
Unlinked-Reads: short range information
Linked-Reads: long range information
Physical Coverage vs. Depth pt.1
Physical Coverage vs. Depth pt.2
Physical Coverage vs. Depth pt.3
Physical Coverage vs. Depth pt.4
Molecule Coverage vs. Read Coverage
Targeted Linked-Reads
Linked Reads for a Range of Variant Types pt.1
Linked Reads for a Range of Variant Types pt.2
Importance of Phasing in Clinical Exome
Compound Heterozygous Variant Resolution pt.1
Compound Heterozygous Variant Resolution pt.2
Linked Reads for a Range of Variant Types pt.3
Standard Short Read Alignment
Long Ranger – Lariat Aligner
Extent of Paralogy in Exomes
Current Clinical Approaches to Homology
Assessing STRC with Linked-Reads
Linked Reads for a Range of Variant Types pt.4
Short Read Approach: Average Depth
10X Approach: Depth by Haplotype
Linked Reads for a Range of Variant Types pt.5
In samples with allele
In samples with an inversion
Visualization of inversion
Complex Structural Variation Detection pt.1
Complex Structural Variation Detection pt.2
Complex Structural Variation Detection pt.3
Complex Structural Variation Detection pt.4
Linked Reads for a Range of Variant Types
View from the Karyotype
View from the Array
Visualization of Event by Linked Reads pt.1
Visualization of Event by Linked Reads pt.2
Visualization of Event by Linked Reads pt.3
Detection of Large SVs at Lower Depths
Abnormal barcode overlap?
Haplotype resolution provides
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