Unable to upload wgs-balsamic to Scout

When using an old yaml-file: /home/proj/production/cancer/cases/toughdingo_2019-xx-xx/analysis/scout/toughdingo.scout.yaml

I am copying and converting and adjusting it to a new yaml-file: /home/proj/production/cancer/cases/fullgibbon/analysis/scout/fullgibbon.scout.yaml

I am unable to upload the last yaml-file since the variant has SOMATIC but not somatic score in the vep-annotated vcf-file:

Traceback (most recent call last):
  File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/scout/adapter/mongo/variant_loader.py", line 643, in load_variants
    sample_info=sample_info,
  File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/scout/adapter/mongo/variant_loader.py", line 429, in _load_variants
    category=category,
  File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/scout/parse/variant/variant.py", line 219, in parse_variant
    parsed_variant["somatic_score"] = int(somatic_score)
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
2020-11-03 14:39:59 hasta.scilifelab.se scout.adapter.mongo.variant_loader[241498] WARNING Deleting inserted variants
2020-11-03 14:39:59 hasta.scilifelab.se scout.adapter.mongo.variant[241498] INFO Deleting old clinical  variants for case fullgibbon_balsamic
2020-11-03 14:39:59 hasta.scilifelab.se scout.adapter.mongo.variant[241498] INFO 633 variants deleted
2020-11-03 14:39:59 hasta.scilifelab.se scout.commands.load.case[241498] ERROR Something went wrong during loading
2020-11-03 14:39:59 hasta.scilifelab.se scout.commands.load.case[241498] WARNING int() argument must be a string, a bytes-like object or a number, not 'NoneType'
Aborted!

[hassanfa]

SV/SNV separation is causing some troubles recently (recent BALSAMIC release doesn’t instruct variant callers to disable SV calls). It is in my backlog to split them properly.

[dnil]

The VCF in question doesn’t even have SOMATICSCORE in the header INFO field, only SOMATIC (very likely from Manta, but unclear why it no longer writes SOMATICSCORE?). And the same goes for the actual variants. To confuse things, the VCF also has a SOMATIC field in the VEP CSQ, but I’m guessing thats a very different, as the INFO one is populated by other means?

When was it last loaded? Must have been some time ago if the VCF didn’t change - the update to cancer SVs was like 9-10 months ago, and this has been handled the same way all that time?

Are you sure you did not simply load only the SNV VCF last time around?