Table 3

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

VarScan

SAMtools

SeqGene


Father

Mother

Daughter

Father

Mother

Daughter

Father

Mother

Daughter


After SNP Filter

696

522

522

539

560

634

637

628

703


Coverage

> 10

After Family Filter

356

(4)

330

(4)

331

(3)

279

(5)

279

(4)

278

(8)

320

(4)

318

(3)

322

(6)


Mendelian Error Rate (%)

1.1

1.2

0.9

1.8

1.4

2.9

1.2

0.9

1.9


After SNP Filter

690

503

506

389

355

413

478

416

472


Coverage

> 20

After Family Filter

340

(4)

316

(4)

319

(3)

180

(2)

182

(2)

178

(1)

223

(1)

223

(1)

223

(1)


Mendelian Error Rate (%)

1.2

1.3

0.9

1.1

1.1

0.6

0.4

0.4

0.4


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

Open Data