Table 6 Results comparison between GT-WGS and BWA + GATK
From: GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service
Mutation type | Unique mutation sites of GT-WGS | Unique mutation sites of BWA + GATK best practice | Common mutation sites | Mutation sites with consistent position but different genotype | ||||
|---|---|---|---|---|---|---|---|---|
Number | Proportion | Number | Proportion | Number | Proportion | Number | Proportion | |
SNP | 3928 | 0.10% | 4443 | 0.11% | 4,067,370 | (99.89%, 99.88%) | 643 | (0.016%, 0.016%) |
INDEL | 646 | 0.08% | 675 | 0.08% | 823,871 | (99.90%, 99.89%) | 197 | (0.024%, 0.024%) |