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We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
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?