Updated analysis: update modules using manta file for v12 release due to column name changes

[jharenza]

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.gz

When do you expect the revised analysis will be completed?

during V12 subtyping

Who will complete the updated analysis?

@jharenza or @ewafula

[jharenza]

Closed with d3b-center/OpenPedCan-analysis#321