This post has some explanation about the use of slash (/) and vertical pipe (|) in GATK's vcf output.
Apparently, a slash (/) indicates that "we don’t know which chromosome they (alleles) are on". If this is the case, why does my VCF have many (virtually all) slashed (/) allele calls for loci with a denoted chromosome and position?
For example,
CM014970.1 4450225 . C T 31.37 . <VARIOUS INFO> 0/0:2,0:2:6:0,6,49 0/0:2,0:2:6:0,6,49 ./.:0,0:0:.:0,0,0
are the called alleles on chromosome CM014970.1 or is it unknown?
I don't understand how that answers the point about not knowing "which chromosome they are on" when loci with slashes have stipulated chromosomal information, e.g.:
To clarify: are the called alleles on chromosome CM014970.1 or is it unknown?