Missing fairly clear indel

[robert-a-forsyth]

Hi,

I've been running clairSTO like so

/opt/bin/run_clairs_to         --tumor_bam_fn sample.bam \
    --ref_fn Homo_sapiens_assembly38.fasta \
    --platform ont_r10_dorado_sup_5khz_ssrs \
    --threads 24 \
    --output_dir sample \
    --conda_prefix /opt/micromamba/envs/clairs-to \
     \

and it seems to still miss quite an obvious deletion here, I'm just wondering what settings I can change which might improve the discovery

[aquaskyline]

this is (very likely) a germline heterozygous 12bp deletion. sto calls somatic variants and ditches germline variants. to call germline variants, please use Clair3.