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Jexl commands; selecting multi or phased alleles
I am looking for a pathogenic variant in exome read data. To identify common inherited regions I would like to extract information from multiallelic sites or variants with phased data. Is there a way to select or filter variants based on this information with JEXL commands. I am familiar with "vc.getGenotype" , but only know how to specify HomRef, HomVar or Het. I would like to distinguish 0/1 from 0/2 or 1/1 from 1/2. Also, it would be very useful to identify if close proximity variants are on the same chromosome. I can read this data from the phased allele calls but is there a way to use Jexl to automate these calls?