Updated analysis: TMB calculation for tumor only WGS

d3b-center / OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project

https://d3b-center.github.io/OpenPedCan-analysis/

Other

15 stars 13 forks source link

Updated analysis: TMB calculation for tumor only WGS #563

Closed jharenza closed 2 weeks ago

jharenza commented 4 months ago

What analysis module should be updated and why?

Add wgs_canonical_calling_regions.hg38.bed to biospecimen_id_to_bed_map.tsv for tumor only WGS samples and rerun

What changes need to be made? Please provide enough detail for another participant to make the update.

What input data should be used? Which data were used in the version being updated?

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

@jharenza

jharenza commented 2 weeks ago

Following tumor only benchmarking with @dmiller15 , we found that the TMB values are not reliable in tumor only variant calling, so we will not do this. Please refer to JIRA ticket: https://d3b.atlassian.net/browse/BIXU-1928