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Table 4 Public call set specific SNPs

From: An analytical workflow for accurate variant discovery in highly divergent regions

Type

Rep

Public call set

No. SNP

  

Cortex

DISCOVAR

GATK HC

Conf

 

Known

1 only

6

13

17

2

21 (11,0)

Known

2 only

3

5

11

4

11 (3,2)

Known

1 & 2

4

18

48

6

57 (33,10)

Novel

1 & 2

1

10

4

0

13 (2,5)

  1. Shown is the number of SNPs in the HLA region of NA12878 that were present in the public call set but missed by GSNAP + GATK UnifiedGenotyper. Cortex, DISCOVAR and GATK HaplotypeCaller (GATK HC) calls were from 250-bp paired sequencing of a PCR-free genomic library [38]. The high-confident call set (“Conf”) was from [36]. See Table 3 footnote for additional information