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Table 5 Comparison of the validation rates of variants called by different pipelines for SureSelect-HiSeq data

From: Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling

 

bwa_pea variants

bwa_seb variants

stampy_sec variants

 

InDels

SNPs

InDels

SNPs

InDels

SNPs

Validated true

93.1 %(108)

90.0 %(117)

93.1 %(108)

86.6 %(110)

92.5 %(99)

88.6 %(101)

Validated false

6.9 %(8)

10.0 %(13)

6.9 %(8)

13.4 %(17)

7.5 %(8)

11.4 %(13)

  1. Note: abwa-pe, bwa mapping with paired-end reads mode
  2. bbwa-se, bwa mapping with single-end reads mode
  3. cstampy-se, stampy-1.0.22 software mapping with single-end reads mode
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BMC Genomics

ISSN: 1471-2164

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