Sample ID
TCGA-CR-7399-01A-11D-2012-08_TCGA-CR-7399-10A-01D-2013-08_mutect_annotated

Sample VCF File
TCGA-CR-7399-01A-11D-2012-08_TCGA-CR-7399-10A-01D-2013-08_mutect_annotated.vcf

Sample VCF Genome
hg38

Sample VCF Total Point Mutations
5,739

FIREVAT Execution Start Datetime
2019-05-15 22:54:03

FIREVAT Execution End Datetime
2019-05-16 01:50:47


FIREVAT Genetic Algorithm (GA) Parameters
GA Population Size 200
GA Maximum Iteration 100
GA Run 100
GA Mutation Probability 0.100

1. Refinement Optimization

Filter Variable Filter Direction Optimized Cutoff
NormalADRef >= 5
NormalADAlt <= 4
AvgNormalRefQSS >= 18
TumorADRef >= 2
AvgTumorRefQSS >= 15
TumorADAlt >= 5
AvgTumorAltQSS >= 14
NormalVAF <= 9
TumorVAF >= 7
Objective Value C.refined W.refined C.artifact W.artifact
0.817 0.979 0.0116 0.992 0.851

2. Optimzed Mutational Signature Identification


2.1. Identified Signatures


2.2. Trinucleotide Spectrums

Original VCF Refined VCF Artifactual VCF
Mutations Count (%) 5,739 (100%) 655 (11.41%) 5,084 (88.59%)
Cosine Similarity Score 0.991 0.973 0.991
Residual Sum of Squares (RSS) 0.00151 0.00116 0.00184
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

## None to display.


4.2. Artifactual VCF

## None to display.

5. VCF Annotation (ClinVar)


5.1. Refined VCF

CHROM POS REF ALT GENEINFO CLNSIG
chr3 179,218,303 G A PIK3CA:5290 Pathogenic/Likely_pathogenic
chr10 94,304,583 C T PLCE1:51196 Pathogenic
chr17 7,674,893 C A TP53:7157 Likely_pathogenic


5.2. Artifactual VCF

CHROM POS REF ALT GENEINFO CLNSIG
chr11 68,780,705 C A CPT1A:1374 Pathogenic