Data issue: incorrect variant type

[rmadupuri]

Variant type must be SNP, INS, DEL, DNP, TNP, MNP, ONP. 3097 cases have no variant types or labeled as NA or UNK. GN JSON contains correct variant types, so reannotation can resolve this.

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 = 'NA' or variant_type = 'UNK';

And below is the count per study:

cancer_study_identifier	count
ucec_ccr_msk_2022	1666
pan_origimed_2020	507
mds_iwg_2022	229
mixed_msk_tcga_2021	206
ucec_ccr_cfdna_msk_2022	176
acc_2019	60
rbl_cfdna_msk_2020	46
coad_silu_2022	28
pancan_pcawg_2020	18
pptc_2019	12
paired_bladder_2022	11
sclc_jhu	10
nsclc_tracerx_2017	9
bowel_colitis_msk_2022	7
hcc_inserm_fr_2015	7
prad_p1000	6
nepc_wcm_2016	5
pediatric_dkfz_2017	5
pog570_bcgsc_2020	5
rectal_msk_2022	5
skcm_broad_brafresist_2012	5
nhl_bcgsc_2013	4
paad_cptac_2021	4
prad_su2c_2019	4
prostate_pcbm_swiss_2019	4
skcm_broad	4
utuc_msk_2019	3
utuc_mskcc_2015	3
cervix_msk_2023	2
cll_iuopa_2015	2
crc_eo_2020	2
mbl_dkfz_2017	2
mtnn_msk_2022	2
npc_nusingapore	2
nsclc_mskcc_2018	2
prad_cpcg_2017	2
sarcoma_mskcc_2022	2
skcm_dfci_2015	2
tmb_mskcc_2018	2
ucs_jhu_2014	2
utuc_cornell_baylor_mdacc_2019	2
utuc_pdx_msk_2019	2
brca_bccrc	1
hcc_jcopo_msk_2023	1
mds_mskcc_2020	1
nbl_msk_2023	1
nccrcc_genentech_2014	1
nsclc_ctdx_msk_2022	1
nsclc_tcga_broad_2016	1
odg_msk_2017	1
paad_icgc	1
paad_qcmg_uq_2016	1
prad_broad	1
prad_fhcrc	1
prad_pik3r1_msk_2021	1
prostate_dkfz_2018	1
sarcoma_msk_2023	1
sclc_ucologne_2015	1
stad_oncosg_2018	1
stad_pfizer_uhongkong	1
stad_tcga_pub	1
ucec_cptac_2020	1