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Table 2 Number of SNPs 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 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