Functional:

• set protein impact to p.? when top effect is SPLICE in coding transcripts

Bugs:

• IMPACT and PAV_TI VCF field count was incorrectly set

Technical:

• handle multiple local phase sets from Sage (in v3.0)
• handle alt missing, * and N, and only use first of multiple allele alts - added to support a Strelka-generated VCF