CNVKit VCF - uses N reference

[davmlaw]

CNV kit writes out VCF records like:

chr1    464423  .   N   <DEL>

We currently reject these in vcf_clean_and_filter.py due to non-standard (ie GATC-containing) reference base.

We should probably just look up the N with the reference base and replace it (which would stop duplication of standard symbolic variants)

Example VCFs are here:

upload/test_data/vcf/cnv/cnvkit.vcf
upload/test_data/vcf/cnv/dragen.cnv.vcf

[davmlaw]

We do use CNVkit in diagnostics, so need this