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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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reference calls for re-genotyping individual sample given (-c) sites #245

Open brentp opened 2 years ago

brentp commented 2 years ago

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

jelber2 commented 1 year ago

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