Documentation for the methylphase toolkit
How do i generate Floria haplotypes?
Use the Floria toolkit to call haplotypes from variant VCFs and BAMs. See the Floria docs for details.
The tool says MM/ML tags are missing.
Ensure your aligner wrote modification tags; some pipelines require --mod-tags or equivalent. Without MM/ML tags, methylphase cannot locate methylation coordinates. We recommend mapping with dorado aligner using BAM files with MM/ML tags. If you prefer minimap2, use -y flag to ensure read-id flags are emitted to the resulting alignment BAM.
The BAM is missing an index.
Create one with samtools index sample.mod.bam.
SEQ is absent in the BAM header.
Provide --sequence-fallback <fastq|bam> (and index the fallback if large) so methylphase can recover base sequences for motif placement.
Too many or few variant calls.
If you observe oversplitting into variants, increase penalty in phase-variants (e.g., --penalty-multiplier 3.0). If you observe too few variants, consider changing the default criterion. The ICL criterion tends produce the least amount of variants; switching to BIC or CV (--criterion bic or --criterion cv) may increase variant calls.
Outputs are huge.
Disable FASTQ/BAM emission during split-reads unless needed (--emit-fastq=false), and limit motifs to those required for the analysis.
How to investigate variant selection.
Inspect fits/ and summary.json for Pi values, these indicate the relative abundance of the variants. Low Pi variants (e.g., < 0.05) may be spurious and can be filtered post-hoc or rerun with adjusted parameters.