WGS variant calling fails when creating SBS96 counts

[Nicklas Nordborg]

The error:

java.lang.RuntimeException: Traceback (most recent call last):
  File "/home/scanb/lorry/jobs/WGSVariantCall-240930-1051-4345-4df359/sbs96.py", line 81, in <module>
    sbsCounts[sbs] = sbsCounts[sbs]+1
KeyError: 'C[C>T]N'

The cause seems to be a variant that is located where the neighbor position has a 'N' in the reference. The context becomes C[C>T]N which is not one of the 96 SBS context. The script needs to be updated to handle this situation (eg. ignore the variant).

[Nicklas Nordborg]

In 7868:

Fixes #1614: WGS variant calling fails when creating SBS96 counts

We only accept ACGT in the TRINUCLEO annotation.