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Cannot get HaplotypeCaller to output phase information in pooled multi-sample calling mode.
There is currently no way to run HaplotypeCaller with pooled multi-sample calling and still get phasing output. By pooled multi-sample calling, I'm referring to running HaplotypeCaller to simultaneously call multiple samples.
There are two scenarios we have attempted which do not work:
1) If HaplotypeCaller is run with emitRefConfidence NONE, it simply does not output any phasing information (seems like a bug).
2) HaplotypeCaller is run with emitRefConfidence GVCF, it does not support pooled multi-sample calling (i.e. the BAMs must only contain reads from one sample per invocation).
We have seen pooled multi-sample calling perform significantly better but would also greatly benefit from HaplotypeCaller's phasing information. Is there a way to get both?