reference calls for re-genotyping individual sample given (-c) sites

[Brent Pedersen]

Hi, I am running octopus with this command in order to genotype a given set of sites:

octopus --threads 12 --ignore-unmapped-contigs  \
    --config ../octopus/resources/configs/PacBioCCS.config  \
    -R $ref38 -I $bam \
    --disable-denovo-variant-discovery \
   -c $sites -o $output

however there are no reference calls in the output. Is there a way to force reference calls (in a single sample) at the sites given in -c?

I looked through the available options, but it looks like the refcall stuff is related to gvcf?
thanks

[Jean Elbers]

Have you tried --refcall POSITIONAL and --keep-unfiltered-calls see #249 (maybe test on a subset of the data?)