phased pileup output incomplete for non-modified bases in haplotype

[SebastianHollizeck]

Hi all,

I am currently attempting to estimate haplotype resolved methylation.

I ran version 0.6.0

modkit pileup -r GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
    --cpg \
    --combine-strands \
    --region chrX \
    --phased \
    --modified-bases C \
    --combine-mods \
    --bgzf \
    CHW_XCI_01.pass.haplotagged.bam \
    methyl/CHW_XCI_01.methyl.cpg.chrX.phased

but on inspecting the files i noticed that not all sites are present in the HP1 and HP2 files.

zgrep -nP "\t19496\t" methyl/CHW_XCI_01.methyl.cpg.chrX.phased/*
combined.bed.gz:335:chrX	19496	19497	C	4	.	19496	19497	255,0,0	4	100.00	4	0	0	2	15	0	1
hp1.bed.gz:331:chrX	19496	19497	C	4	.	19496	19497	255,0,0	4	100.00	4	0	0	2	6	0	0

This position is missing from the hp2 file.

Screenshot of the location.

This seem unintentional, but maybe I am missing something.