SV report fixes

[Madelinehazel]

• Change snpEff database to GRCh38.86 so that VCF is annotated with Ensembl genes/transcripts
• Modify annotate_counts so that if there is no overlap between the sample SVs and the count table (i.e. for BNDs annotated against the Manta MSSNG database, which does not contain BNDs), the column is just populated with '-'. We could instead use a lifted over file from GRCh37 in the future if desired, as this does contain BND counts
• The columns associated with the MSSNG count are named after the file name, so for example the Manta SV column becomes "noBNDs_includeHQsamples_mssngSubjetsCounts_hiseqX_mantaSVs_db6_hg38_1based_FIXEDCOLUMNS_sorted_nochr_uppertype"; may want to reconsider renaming these files to something more comprehensible

[NourHanafi]

Thanks for your help on this Madeline! It is now ready to merge. Tested and made changes to the SV workflow.

Also, unrelated to SVs but involving the hg38 pipeline: changed the reference from Illumina to GIAB, and incorporated the C4R exome counts into the vcfanno annotation pathway (other changes for this found in the cre hg38 branch).