TRON-Bioinformatics/covigator-ngs-pipeline: v0.17.0

Changes Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These are annotated in the field INFO/problematic. Also, all mutations at beginning and end of the genome are now filtered out. Changes the default VAFs to classify mutations and introduces a new classification. Low frequency are those below 2 % VAF, subclonal are above or equal 2 % and below 50 %, low quality clonal are above or equal 50 % and below 80 %; the rest are considered clonal