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How to call variance with Haplotype Caller on just one chromosome?
I am trying to just call variance using Haplotype Caller on only chr1 in a horse, on 8 samples. Do I need to split the BAM files by chromosome or can I simply ask Haplotype Caller to just call variance on just one chromosome? I am guessing I need to do the former, as I can not find the answer to the latter.
Thanks in advance.