Data Issue: INDELs annotated as SNPs

[rmadupuri]

Variants with common prefixes have issues when being annotated. Needs preprocessing to fix alleles, coordinates.

https://docs.google.com/spreadsheets/d/1Krb7t80nJ5fZcmUdPLGvmf4BBh4oL4FEnc42QA_Zw6M/edit#gid=0

select * from mutation_event
where length(reference_allele) != length(tumor_seq_allele)
and variant_type not in ('INS', 'DEL');

at study level:

select cs.cancer_study_identifier, me.*
from mutation_event as me
join mutation as m on me.mutation_event_id = m.mutation_event_id
join genetic_profile as gp on m.genetic_profile_id = gp.genetic_profile_id
join cancer_study as cs on gp.cancer_study_id = cs.cancer_study_id
where variant_type not in ('INS', 'DEL')
and length(reference_allele) != length(tumor_seq_allele);

A couple of these can be fixed with reannotation with GN.