Table 2

Number of SNPs and Mendelian error rates using Varscan, SAMtools and SeqGene

VarScan

SAMtools

SeqGene


Father

Mother

Daughter

Father

Mother

Daughter

Father

Mother

Daughter


After SNP Filter

26458

19814

20788

39657

24384

26971

23522

22776

24097


Coverage

> 10

After Family Filter

16037

(235)

14392

(145)

15048

(194)

15775

(375)

13174

(324)

13556

(458)

15678

(131)

15541

(128)

15809

(191)


Mendelian Error Rate (%)

1.5

1.0

1.3

2.3

2.4

3.6

0.8

0.8

1.2


After SNP Filter

23444

16317

17639

27814

15797

18060

18805

16354

17889


Coverage

> 20

After Family Filter

13992

(124)

12594

(93)

13244

(147)

9745

(90)

8522

(93)

8674

(140)

12001

(63)

11887

(53)

12202

(89)


Mendelian Error Rate (%)

0.9

0.7

1.1

0.9

1.1

1.6

0.5

0.4

0.7


Deng BMC Bioinformatics 2011 12:267   doi:10.1186/1471-2105-12-267

Open Data