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Table 1 The 26 SNV calling pipelines

From: Similarities and differences between variants called with human reference genome HG19 or HG38

Number Aligner GATK recalibration Caller
1 Novoalign N FreeBayes
2 Novoalign N HC
3 ISAAC N FreeBayes
4 ISAAC Y FreeBayes
5 ISAAC N HC
6 ISAAC Y HC
7 ISAAC N ISAAC
8 ISAAC Y ISAAC
9 ISAAC N SAMtools
10 ISAAC Y SAMtools
11 BWA N FreeBayes
12 BWA Y FreeBayes
13 BWA N HC
14 BWA Y HC
15 BWA N ISAAC
16 BWA Y ISAAC
17 BWA N SAMtools
18 BWA Y SAMtools
19 Bowtie2 N FreeBayes
20 Bowtie2 Y FreeBayes
21 Bowtie2 N HC
22 Bowtie2 Y HC
23 Bowtie2 N ISAAC
24 Bowtie2 Y ISAAC
25 Bowtie2 N SAMtools
26 Bowtie2 Y SAMtools