Converted to:
NC_000002.11:g.215632255_215632256delinsTG
When submitting this to the variant validation service we get the following error:
Unexpected error processing :NC_000002.11:g.215632255_215632256delinsTG; 'Inv' object has no attribute 'alt'
Seeing that error, the variant might actually be an inversion, which would mean that we need to write it like:
NC_000002.11:g.215632255_215632256inv
However, looking at the reported variant, this is probably not an inversion.
Reference genome from 215632253-215632257:
CACATG
Complementary stand:
GTGTAC
Taking a look at the complementary strand suggests it might be an inversion (GT>TG), but if the variant is on the forward strand (CA>TG), it isn't. We need to look into that and find out what the actual variant is.
To do:
1) Find out if the variant is an inversion
2) Write code that creates proper HGVS g for inversions
3) Find out why the variant validator won't take this variant, whether it's an inversion or not
4) Find out what happens with other inversions:
a. check for the delins notation
b. check for the proper inv notation
5) Find out how we can properly process correct variants and report invalid ones
Converted to:
NC_000002.11:g.215632255_215632256delinsTGWhen submitting this to the variant validation service we get the following error:
Unexpected error processing :NC_000002.11:g.215632255_215632256delinsTG; 'Inv' object has no attribute 'alt'Seeing that error, the variant might actually be an inversion, which would mean that we need to write it like:
NC_000002.11:g.215632255_215632256invHowever, looking at the reported variant, this is probably not an inversion.
Reference genome from 215632253-215632257:
CACATGComplementary stand:GTGTACTaking a look at the complementary strand suggests it might be an inversion (GT>TG), but if the variant is on the forward strand (CA>TG), it isn't. We need to look into that and find out what the actual variant is.To do:
1) Find out if the variant is an inversion 2) Write code that creates proper HGVS g for inversions 3) Find out why the variant validator won't take this variant, whether it's an inversion or not 4) Find out what happens with other inversions: a. check for the delins notation b. check for the proper inv notation 5) Find out how we can properly process correct variants and report invalid ones