Data issue: incorrect stop positions

[rmadupuri]

For SNPs:

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 in ('SNP', 'DNP', 'TNP', 'MNP', 'ONP')
and end_position != start_position + length(tumor_seq_allele)-1;

Most of these variants have common prefixes which once removed are either INS, DELs but are annotated as SNPs.

metastatic_solid_tumors_mich_2017 36
prad_fhcrc 10
sclc_cancercell_gardner_2017 8
msk_impact_2017 5
acc_2019 4
histiocytosis_cobi_msk_2019 3
mrt_bcgsc_2016 2
msk_ch_2020 2
pan_origimed_2020 2
skcm_yale 2
tmb_mskcc_2018 2
acyc_mda_2015 1
luad_tsp 1
mds_iwg_2022 1
mds_mskcc_2020 1
msk_met_2021 1
pog570_bcgsc_2020 1

For INS type: 93 studies affected.

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 = 'INS'
and end_position != start_position + 1;

For DELs:

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 = 'DEL'
and end_position != start_position + length(reference_allele)-1;

coadread_tcga_pan_can_atlas_2018 6
cscc_ucsf_2021 3
stad_tcga_pan_can_atlas_2018 3
gbm_tcga_pan_can_atlas_2018 2
lusc_cptac_2021 2
all_stjude_2015 1
blca_tcga_pan_can_atlas_2018 1
cesc_tcga_pan_can_atlas_2018 1
crc_msk_2017 1
hnsc_tcga_pan_can_atlas_2018 1
mbl_dkfz_2017 1
ov_tcga_pan_can_atlas_2018 1
sarcoma_mskcc_2022 1