Sample ID
DCC_PCAWG_Cell_Lines_HCC1954

Sample VCF File
DCC_PCAWG_Cell_Lines_HCC1954.vcf

Sample VCF Genome
hg19

Sample VCF Total Point Mutations
62,176

FIREVAT Execution Start Datetime
2019-10-22 09:05:03

FIREVAT Execution End Datetime
2019-10-22 12:53:59


FIREVAT Genetic Algorithm (GA) Parameters
GA Population Size 100
GA Maximum Iteration 20
GA Run 20
GA Mutation Probability 0.100

1. Refinement Optimization

Filter Variable Filter Direction Optimized Cutoff
ControlVAF <= 1
TumorVAF >= 4
MappingQuality >= 35
ControlDPRef >= 5
ControlDPAlt <= 3
TumorDPRef >= 0
TumorDPAlt >= 6
Objective Value C.refined W.refined C.artifact W.artifact
0.806 0.995 0.116 0.978 0.938

2. Optimzed Mutational Signature Identification


2.1. Identified Signatures


2.2. Trinucleotide Spectrums

Original VCF Refined VCF Artifactual VCF
Mutations Count (%) 62,176 (100%) 19,425 (31.24%) 42,751 (68.76%)
Cosine Similarity Score 0.978 0.94 0.978
Residual Sum of Squares (RSS) 0.00626 0.00201 0.0127
2.2.1. Observed Spectrum

2.2.2. Maximum-likelihood Estimation (MLE) Reconstructed Spectrum

2.2.3. Residual Spectrum


2.3. Nucleotide Substitution Types

3. Optimized VCF Statistics

4. Variants with Strand Bias


4.1. Refined VCF


4.2. Artifactual VCF

5. VCF Annotation (ClinVar)


5.1. Refined VCF


5.2. Artifactual VCF