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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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Add germline sex estimate to bixops file #523

Closed jharenza closed 1 year ago

jharenza commented 1 year ago

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

bixops file - perhaps there is a more recent one than 20230203_release_histologies_ops_update.csv which includes these samples - if so, please send me a link to it.

What release are you using?

20230203_release_histologies_ops_update.csv

Put your question or report your issue here.

The following samples are missing from the ops file for germline sex estimate. Assuming paired tumor would also be missing tumor fraction/ploidy - can you please add? missing_germline_sex.csv

cc @zhangb1 @HuangXiaoyan0106

HuangXiaoyan0106 commented 1 year ago

@jharenza These samples were not recorded in the 2023-02-02_histologies-base.csv, and gender estimation only updates the existing sample information in the base histology without adding new sample records. Therefore, there will be no gender records of these samples in the bixops file.

The calculation of tumor fraction/ploidy is independent and does not intersect with gender prediction. As long as the tumor samples are in the histology and have genomics files, there will be calculation results.

Based on this ticket, I checked the BS ids you provided and calculated the sex results. Then, I matched the samples in histology file using the Kids_First_Participant_ID and updated the germline_sex_estimate information. add_germline_sex.csv

@zhangb1 updated histology file: https://cavatica.sbgenomics.com/u/d3b-bixu-ops/monthly-release-analysis/files/64083bc48de76763cec8c463/

jharenza commented 1 year ago

Thanks, that makes sense! I just updated histologies again, given the new harmonized data, so here it is https://github.com/d3b-center/histologies-qc/blob/69ea59bc1dba8e84e398ae63a36de51a8eb7e30a/output/2023-03-08_histologies-base.tsv