HSiga commented 3 years ago

Adding some Structural variants implementation

pontushojer commented 3 years ago

So some things we need to fix here:

I have with https://github.com/NBISweden/BLR/commit/9dcbc4326f195db7461aa03aaf787838b4c0ff4d fixed the BEDPE formatting of the NAIBR output so that it matches LinkedSV output. Therefor the scripts convert_reformat_bedpe_naibr.bash and refromat_naibr_output.R are no longer needed.
Remove conda-pack from environment.yml.
Move the rule for LinkedSV calling into phasing.smk to put it together with NAIBR.
Go through the options in blr.yaml. Atm only min_supp_barcodes is actually used. I think we should make the save_temp_files option active since this might be useful. The others I cannot see the use in changing for now. These options will also have to added to the config.schema.yaml to be validated.

I also started a bit on the LinkedSV integration, you can look at my work in this branch https://github.com/NBISweden/BLR/compare/linkedsv-integration. I think we should combine this with your version.

HSiga commented 3 years ago

44 will be used for linkedSV integration instead.

AfshinLab / BLR