NGS Flashcards

1
Q

FFPE artifacts

A

C>T or G>A

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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

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3
Q

How do you calculate the VAF?

A

Number of “clean” reads divided by total number of reads

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4
Q

When do you suspect an FFPE artifact?

A

G>A, C>T

VAF<0.20

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5
Q

PHRED score of 10
Chance of error?
Accuracy?

A

1 in 10

90%

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6
Q

PHRED score of 20
Chance of error?
Accuracy?

A

1 in 100

99%

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7
Q

PHRED score of 30
Chance of error?
Accuracy?

A

1 in 1000

99.9%

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8
Q

PHRED score of 40
Chance of error?
Accuracy?

A

1 in 10000

99.99%

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