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 |