Why are the frequencies different from the ones in my input VCF?

[Paururo]

I gave get_MNV a VCF that already carries allele frequencies, plus a BAM. The
frequencies in the output do not match the ones my caller wrote.

Which of the two is right, and did I lose the original numbers?

[Paururo]

Both are right. They answer different questions.

Your caller's frequency is what it computed for a position. With --bam,
get_MNV counts again from the alignments, and it counts per event: per SNV,
per MNV haplotype, and per indel event.

That last distinction is where the numbers usually part company. The frequency of
an MNV haplotype is not the frequency of either change in it: it is the fraction
of reads carrying both, which is normally lower than either one alone. A
position-wise number cannot express that, because the thing being measured spans
more than one position.

You have not lost anything. The values that came in are kept as OFREQ and
ODP, beside the recounted ones, so you can compare them directly.

And without --bam nothing is recounted at all: what you passed in is what comes
out.