Updated analysis: Expand the 50% reciprocal overlap to include complete overlap of 1 CNV by other larger CNV

[kgaonkar6]

Work on this after/with #132

What analysis module should be updated and why?

We believe criteria for cnvs to have 50% reciprocal overlap might be too stringent. After the #1116 we are missing some subtype defining CNVs.

Propogating changes from AlexsLemonade/OpenPBTA-analysis#1125

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

After investigation we see the CNV alterations n controlfreec and cnkit . For example chr19 amplification in BS_K07KNTFY
is seen in both controlfreec and cnvkit but missed out of consensus calls because cnvkit region is 11% of controlfreec region

BS_K07KNTFY.cnvkit.dup.filtered3.bed: chr19	54138551	54427104
BS_K07KNTFY.freec.dup.filtered3.bed:  chr19	53641020	56141391

What was your approach?

Our approach was to broaden the criteria to include CNV calls in either caller that has any overlap at this step
master
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/2511e8c9fc4a7542f5b709363f866ccddb73be8b/analyses/copy_number_consensus_call/scripts/compare_variant_calling_updated.py#L148-L152

consensus-cnv-smallCNV-overlap

                        ## For list2's CNV
                        ## If any overlap exists,
                        ## then we add in the start, end coordinate, total overlap length, and total len to different lists
                        ## This is done to account for 1 CNV from list1 overlapping with MULTIPLE CNVs from list2
                      if (end - start +1) / (end_list2 - start_list2 + 1) >= 0:

And at the following snippet we allow CNV overlaps that completely overlap a smaller CNV in caller X by a larger CNV in callerY
master
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/2511e8c9fc4a7542f5b709363f866ccddb73be8b/analyses/copy_number_consensus_call/scripts/compare_variant_calling_updated.py#L181

consensus-cnv-smallCNV-overlap

if (coverage_list1 >= 0.5 and coverage_list2 >= 0.5) or (coverage_list1 >=0.9 and coverage_list2 >0 ) or (coverage_list1>0 and coverage_list2 >=0.9):

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

pbta-cnv-cnvkit.seg.gz
pbta-cnv-controlfreec.tsv.gz
pbta-sv-manta.tsv.gz

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

[jharenza]

closed with d3b-center/OpenPedCan-analysis#77