Include the ReferenceBases annotation when running Mutect2

[Nicklas Nordborg]

This is a configuration change only. We should add --annotation ReferenceBases to the !Mutect2Options setting in reggie-config.xml.

This will add an INFO-level annotation REF_BASES to the VCF file that contain 21 bases. 10 bases before and after the REF with the REF in the middle.

From this annotation we can modified the vcfanno configuration to extract the middle 3 bases and store it as a separate annotation. This information is already in the RNAseq variant calling with name TRINUCLEO so we will use the same.

[Nicklas Nordborg]

In 7481:

References #1552: Include the ReferenceBases annotation when running Mutect2

Added --annotation ReferenceBases to reggie-config.xml.