Yichao Sun

Investigate high TMB for cscc_hgsc_bcm_2014

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When calculating TMB for all public studies, we found `cscc_hgsc_bcm_2014` with unexpected high TMB scores (see this PR: https://github.com/cBioPortal/datahub/pull/1428). Altho in MAF all mutations are marked at `somatic`, some mutations...

Ambiguity in the matched normal status for `ucec_cptac_2020`. Details in this PR comments: https://github.com/cBioPortal/datahub/pull/1506

Circle CI bug: database creating/dropping issue between commits

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Validation error in PR https://github.com/cBioPortal/datahub/pull/1613 In Circle CI test server local database, the row with value `null` in `info` table, possibly from one of earlier `seedDB.sql.gz` commits, didn't get dropped...

Mutated Issue: Annotator jar unable to annotate DNP & TNP variants

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When annotating DNP/TNP (Double nucleotide polymorphism/Triple nucleotide polymorphism) variants, we could get results from Genome Nexus API. However, when running annotator jar sending empty MAF as input, we don't get...

Mutated Issue: "Splice Region" always get picked as variant class

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When having multiple consequences and if `splice_region_variant` is presented, annotator/GN always picks/adds "Splice Region" as the variant class, even if other consequences are "3'UTR", "5'UTR", "intron" and no protein change...