Sample ID
TCGA-44-2662-01B-02D-A271-08_TCGA-44-2662-10A-01D-A271-08_mutect_annotated

Sample VCF File
TCGA-44-2662-01B-02D-A271-08_TCGA-44-2662-10A-01D-A271-08_mutect_annotated.vcf

Sample VCF Genome
hg38

Sample VCF Total Point Mutations
2,592

FIREVAT Execution Start Datetime
2019-10-15 17:38:52

FIREVAT Execution End Datetime
2019-10-15 18:56:36


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
NormalADRef >= 1
NormalADAlt <= 5
AvgNormalRefQSS >= 13
TumorADRef >= 1
AvgTumorRefQSS >= 31
TumorADAlt >= 3
AvgTumorAltQSS >= 12
NormalVAF <= 10
TumorVAF >= 0
TLOD >= 4
Objective Value C.refined W.refined C.artifact W.artifact
0.288 0.988 0.0712 0.982 0.32

2. Optimzed Mutational Signature Identification


2.1. Identified Signatures


2.2. Trinucleotide Spectrums

Original VCF Refined VCF Artifactual VCF
Mutations Count (%) 2,592 (100%) 642 (24.77%) 1,950 (75.23%)
Cosine Similarity Score 0.982 0.984 0.97
Residual Sum of Squares (RSS) 0.000937 0.00158 0.00177
2.2.1. Observed Spectrum

2.2.2. Maximum-likelihood Estimaation (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