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ACEseq - Allele-specific copy numbers from sequencing
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Installation & Run instructions
The Manual Way
Docker version
Reference files
Legacy Installations
QuickStart
Requirements
Hardware
Software
Alternative Running Modes
Run With “Fake” Control
Run Without Control
Run quality check only
Replace low quality control
Run with/without SV breakpoint incorporation
Input Parameters
Purity Evaluation
Quality check
Final Output
HRD, LST, TAI
Methods - Theory
Pre-processing
GC-/Replication timing bias correction
Segmentation
Segment reliability
Segment clustering and merging
Allelic adjustment
Calling of Allelic Balance and Imbalance
Copy Number Estimation
Purity and ploidy estimation
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