Is CpG status predicted at insertion variants?

[elcortegano]

Following a recent issue open in the IGV site (https://github.com/igvteam/igv/issues/1303), we wonder if aligned_bam_to_cpg_scores.py would call 5mC methylated CpG sites at insertions (i.e. at sites that are not in the reference).

I run primrose in my data on the CCS reads, and then 5mC sites were called from a pbmm2 aligned BAM similarly as:

python3 aligned_bam_to_cpg_scores.py \
    -b sample.5mc.pbmm2.bam \
    -f reference.fa \
    -o founders \
    -p model \
    -c 5 \
    -d pileup_calling_model/ \
    -t 16