From: Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success
Discovery method
Predicted validation success (%)
Infinium
Axiom
Predictive
Filtering
BOWTIE2
75.7
45.6
83.3
61.7
BWA
72.1
39.7
78.5
54.6
NEWBLER
46.8
27.3
48.9
35.5
SWAP454
57.0
34.6
61.8
45.9