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How to call SNP without confidence SNP ？
I have WGS data of 100 samples. There's few people work on my species,so I didn't find confidence SNP set to use.
I follow the best-practices of GATK. And my question is how to get convinced SNP from my data ? For I see there is a --db snp in the tool HaplotypeCaller.
By the way, someone told me I can call variants by different software and take the same part as my known sites. Does it work?