Allele Specific QC filtering at multi-allelic sites

[jjfarrell]

What is the best approach for QC of multi-allelic variant in a GLnexus pVCF? If there is one high quality alternate allele and a poor quality allele at a multi-allelic site, how are they filtered properly? In GATK VQSR, there is now a Allele Specific INFO field (AS_FilterStatus) to filter on. Is there something comparable with GLnexus?