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Updated analysis: update modules using manta file for v12 release due to column name changes
#499
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What analysis module should be updated and why?
See ticket here for reference
What changes need to be made? Please provide enough detail for another participant to make the update.
LGAT subtyping (cc @sickler-alex @runjin326 and @aadamk)
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/f944ab52ed7fbd48e70aff42caeda864714e8d8c/analyses/molecular-subtyping-LGAT/03-subset-cnv-files-LGAT.Rmd#L145-L178
TP53 classifier
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/f944ab52ed7fbd48e70aff42caeda864714e8d8c/analyses/tp53_nf1_score/04-tp53-sv-loss.Rmd#L92-L108
chromothripsis
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/f944ab52ed7fbd48e70aff42caeda864714e8d8c/analyses/chromothripsis/01-process-sv-file.R#L43-L198
chromosomal instability
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/f944ab52ed7fbd48e70aff42caeda864714e8d8c/analyses/chromosomal-instability/00-setup-breakpoint-data.R#L213-L237
What input data should be used? Which data were used in the version being updated?
manta-sv.tsv.gzWhen do you expect the revised analysis will be completed?
during V12 subtyping
Who will complete the updated analysis?
@jharenza or @ewafula
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