I'm trying to call snp and with multi-sample plant data. I'll appreciate it if you have any suggestions for the following two questions:
1.It looks that mutect2 is the tool for somatic snp and indel calling, but it's more specific for tumor or other human samples. So should I use Haplotypecaller of mutect2?
2. Are there any suggestions for building a known SNP dataset myself?
Thanks for your time and looking for your reply.
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