Variant calling: number of individuals vs. depth of read coverage Gabor T. Marth Boston College...

Variant calling: number of individuals vs. depth of read coverage

Gabor T. MarthBoston College Biology Department

1000 Genomes MeetingCold Spring Harbor LaboratoryMay 5-6. 2008

Single-base variant calling in 1000G data

1. SNP discovery (for potential follow-up genotyping)

2. Possibly using genotypes called from sequence directly for haplotype phasing (genotype imputation?)Sample size x read coverage / individual = constant

What is the best sample size?Not easy to answer only based on idealistic theoretical considerationsSimulation studies must model many effects to be realistic

Variant discovery is a complex process

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seq. readssamples fragmentspopulation

genotype priors

allele sampling likelihoods

base error probabilities


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G1

G2

G3

Bayesian variant detection math

1 2

1 21

1

1 2

Pr | Pr | Pr , , ,

Pr | Pr | Pr , , ,

Pr , , , |i

kT

i i nl kT

nk ki i i n

i

nk k l l l li i

iG

n

B T T G G G G

B T T G G G G

G G G B

Priors: (1) Nucleotide diversity; (2) Allele frequency distribution; (3) Specific diploid genotype layoutAllele sampling likelihoods: Binomial distribution of the number of reads from each of the two chromosomesBase error probabilities: Likelihood that the called base faithfully represents DNA fragment, calculated from the base quality values

SNP calling and genotyping

P(SNP) = total probability of all non-monomorphic genotype combinations

P(Gi) = marginal probability

consequence: data from other individuals influence the genotype call of a given individual: include illustration using testProb program in GigaBayes package.

Variant calling in simulated data: design

Analysis by Aaron Quinlan(see poster at the Genome Meeting)

Estimated vs. population allele frequency

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5

Expected minor allele frequency

Obs

erve

d m

inor

alle

le fr

eque

ncy 100 Inds @ 16X

corr = 0.89

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 100 Inds @ 16X

corr = 0.89

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 200 Inds @ 8X

corr = 0.92

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 200 Inds @ 8X

corr = 0.92

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 400 Inds @ 4X

corr = 0.93

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 400 Inds @ 4X

corr = 0.93

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 800 Inds @ 4X

corr = 0.91

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 800 Inds @ 4X

corr = 0.91

Allele frequency (cont’d)

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 800 Inds @ 4X

corr = 0.91

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5


Obs

erve

d m

inor

alle

le fr

eque

ncy 800 Inds @ 4X

corr = 0.91

0.005 0.01 0.015 0.02 0.025 0.03 0.035 0.04 0.045 0.05

0.005

0.01

0.015

0.02

0.025

0.03

0.035

0.04

0.045

0.05

SNP discovery sensitivity

Genotype density

0 5000 10000 15000 20000 25000 30000 35000 40000 45000 500000

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

SNP Position

Frac

tion

of c

onfid

ent g

enot

ypes

0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5

x 104

0

200

400

600

800

1000

1200

1400

1600

100 @ 16x: 0.975 +/- 0.121

200 @ 8x: 0.968 +/- 0.129

400 @ 4x: 0.924 +/- 0.151

800 @ 2x: 0.769 +/- 0.154

Genotype density

Fraction of samples w/ confident genotype Fraction of samples w/ confident genotype

Fraction of samples w/ confident genotypeFraction of samples w/ confident genotype

Num

ber o

f SN

PsN

umbe

r of S

NPs

Num

ber o

f SN

PsN

umbe

r of S

NPs

0 0.2 0.4 0.6 0.8 10

1000

2000

3000

4000

0 0.2 0.4 0.6 0.8 10

1000

2000

3000

4000

0 0.2 0.4 0.6 0.8 10

500

1000

1500

2000

2500

3000

0 0.2 0.4 0.6 0.8 10

500

1000

1500

100 Inds @ 16X 200 Inds @ 8X

400 Inds @ 4X 800 Inds @ 2X

Fraction of samples w/ confident genotype Fraction of samples w/ confident genotype

Fraction of samples w/ confident genotypeFraction of samples w/ confident genotype

Num

ber o

f SN

PsN

umbe

r of S

NPs

Num

ber o

f SN

PsN

umbe

r of S

NPs

0 0.2 0.4 0.6 0.8 10

1000

2000

3000

4000

0 0.2 0.4 0.6 0.8 10

1000

2000

3000

4000

0 0.2 0.4 0.6 0.8 10

500

1000

1500

2000

2500

3000

0 0.2 0.4 0.6 0.8 10

500

1000

1500

100 Inds @ 16X 200 Inds @ 8X

400 Inds @ 4X 800 Inds @ 2X

Summary / Conclusions

Thanks

Variant calling: number of individuals vs. depth of read coverage Gabor T. Marth Boston College...

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