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Table 3 Number of indels and Mendelian error rates using Varscan, SAMtools and SeqGene

From: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

   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