Discrepancy between number of SNVs and count of signatures

[kmavrommatis]

Hi,
i am working with a VCF file containing 2950214 records.
This is the output of filtering by bcftools for high quality snps, and after normalization, i.e. multiallelic events are split to separate records.
After running helmsman I get the output with a total of 4329064 events distributed in various triplets

The command line I run is:

python /opt/helmsman-1.5.3/helmsman.py --input test.filter.vcf.gz --fastafile genome.fa -w --mode vcf -m test --projectdir .

For comparison running the equivalent process with R MutationalPatterns results in the expected number of events (i.e. the sum of all triplet events is the same as the input vcf)

Am I missing something here?
Thanks