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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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The difference of variant call files for DNA sample between v11 and v12 release #549

Closed zzgeng closed 1 year ago

zzgeng commented 1 year ago

What data file(s) does this issue pertain to?

variant-level-snv-consensus-annotated-mut-freq.tsv.gz from v11 and v12 https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/dev/analyses/hotspots-detection/input/hotspots_database/hotspot_database_2017_snv.tsv

What release are you using?

v11 and v12

Put your question or report your issue here.

Compare between v11 and v12 release, if there is anything off in protein change (HGVSp_short), transcripts, etc.

jharenza commented 1 year ago

@zzgeng can you take this MAF, which was the original hg19 hotspot VCF lifted over from hg19 to hg38 and then annotated and identify what differences in protein location change by gene from this hotspot TSV file we have been using? We know BRAF protein location will differ, but I think we need to use this as our new comparison. You can use this hotspot file with gene symbols lifted.

jharenza commented 1 year ago

@migbro has been working on this over in bixu-tracker.