NGS Flashcards
1
Q
FFPE artifacts
A
C>T or G>A
2
Q
Characteristics of a false call
A
reads with SNV have additional variants
all mismatches on only one strand
Mismatches near end of read
3
Q
How do you calculate the VAF?
A
Number of “clean” reads divided by total number of reads
4
Q
When do you suspect an FFPE artifact?
A
G>A, C>T
VAF<0.20
5
Q
PHRED score of 10
Chance of error?
Accuracy?
A
1 in 10
90%
6
Q
PHRED score of 20
Chance of error?
Accuracy?
A
1 in 100
99%
7
Q
PHRED score of 30
Chance of error?
Accuracy?
A
1 in 1000
99.9%
8
Q
PHRED score of 40
Chance of error?
Accuracy?
A
1 in 10000
99.99%
