unknown phenotype

[axz91]

if only one allele is being called, /1 , is this unknown or het how to distinguish /1 and */0

[brentp]

you can think of it as the integer number of alts. /1 is 1 alternate allele, /0 is 0 alternate alleles. You can access this with variant.alts

[axz91]

could you provide an example

[brentp]

variant.alts == 1 is true for */1 and false for */0

[axz91]

Thanks! "sample attributes for hom_ref, het, hom_alt, unknown which are synonums for sample.alts of 0, 1, 2, -1 respectively." Could you confirm if sample.alts = -1, all /1 /0 1/ 0? will be called?

[brentp]

• samples.alts == 1 for */1 and 1/*
• samples.alts == 0 for */0 and 0/*