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Arguments for HaplotypeCaller or GenotypeGVCFs
If I want the variants to be called only if they fit the following criteria:
1) Min. total coverage for consideration of heterozygous is 10.
2) Min. coverage of each of the two observed major basecalls to be called heterozygous is 5.
3) Min. percentage of each of the two observed major basecalls in order to be called heterozygous is 20.
4) Min. coverage in order for a position to be called homozygous is 6.
which command-line arguments in which tools (HaplotpyeCaller or GenotypeGVCFs) can I use to accomplish these?
I cannot seem to find the proper arguments in the documentation. I apologize if I overlook.