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GenotypeGVCFs --only-output-calls-starting-in-intervals combined with -L . What does that mean?
the documentation for GenotypeGVCFs argument
Restrict variant output to sites that start within provided intervals
This option can only be activated if intervals are specified.
I am using GenotypeGVCFs repeatedly on every non-overlapping interval
-L foo-bar to cover the genome. Does that documentation mean that for calls which "straddle" two consecutive intervals A and B, the calls will be present in the tail end of A.vcf, and not in B.vcf? Is that the correct way to interpret the manual?
Similarly, if I omitted
--only-output-calls-starting-in-intervals, would that mean that the calls are duplicated VCFs if they land on the edge of two intervals?