Utility commands

methylphase utils <subcommand> provides supporting tools for inspection and downstream use. These command are mostly for internal use but may be helpful for users.

vcf

Summarize motif methylation to VCF (optionally bgzip+tabix).

methylphase utils vcf \
  --bam sample.mod.bam \
  --motif CG_5 \
  --output calls.vcf.bgz \
  --plain-output \
  --sample-name sample1

impute-bam

Impute bases/qualities directly into a BAM using methylation probabilities.

methylphase utils impute-bam \
  --bam sample.mod.bam \
  --motif CG_5 \
  --output imputed.bam \
  --prob-threshold 0.5

contigs

List contigs in a BAM (with optional lengths).

methylphase utils contigs --bam sample.mod.bam

reads

List read IDs for selected contigs (optionally capped).

methylphase utils reads --bam sample.mod.bam --contig chr1 --limit 1000

longitudinal

Compute longitudinal methylation agreement across contigs/bins.

methylphase utils longitudinal \
  --bam sample.mod.bam \
  --motif-file motifs.tsv \
  --output longitudinal.tsv