GPTomics/bio-long-read-sequencing-haplotype-phasing

Version Compatibility

Reference examples tested with: whatshap 2.3+, longphase 1.7+, samtools 1.19+, tabix/htslib 1.19+.

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

Behavior to record:

• whatshap phase --reference enables realignment mode (rescues indel phasing on error-prone long reads); omitting it falls back to lower-quality genotype-only phasing.
• Phasing the VCF and haplotagging the BAM are SEPARATE steps; downstream read-level tools need the BAM HP tag.
• --max-coverage 15 (WhatsHap) is a runtime downsampling cap, not a minimum-depth requirement.

If code throws an error, introspect the installed tool (whatshap phase --help, longphase --help) and adapt the example to the actual API rather than retrying.

Read-Backed Haplotype Phasing

"Phase my long-read variants" -> Reconstruct haplotypes directly from reads that span heterozygous sites, then haplotag the BAM so downstream tools can see the phase.

• CLI: whatshap phase -o phased.vcf.gz --reference ref.fa --indels variants.vcf.gz aln.bam then whatshap haplotag -o haplotagged.bam --reference ref.fa phased.vcf.gz aln.bam

This is read-backed (physical, panel-free) phasing of a single sample. Statistical/reference-panel phasing for imputation lives in phasing-imputation/haplotype-phasing; building phased haplotype contigs lives in genome-assembly/hifi-assembly.

The Single Most Important Modern Insight -- Phasing the VCF Is Useless Until the BAM Is Haplotagged, and Blocks Break Where No Read Spans Two Hets

Read-backed phasing is sample-intrinsic and panel-free (the haplotypes are exactly what this individual's reads physically witness), with two load-bearing consequences:

1. phase writes the VCF; haplotag writes the BAM - they are different products. whatshap phase / longphase phase set GT pipe (0|1) and a PS phase-set in the VCF; they do NOT touch the BAM. Every read-level downstream tool (modkit --partition-tag HP for allele-specific methylation, pb-CpG-tools --hap-tag HP, Severus for phased SVs, IGV color-by-HP, whatshap split) keys on the per-read HP tag that ONLY haplotag writes. A user who runs phase and stops has a phased VCF and an un-haplotagged BAM, and the downstream step silently produces only an ungrouped partition. Triage: samtools view haplotagged.bam | grep -m1 'HP:i:'.
2. Phase blocks break wherever no single read spans two adjacent hets. Block length is capped by read length x heterozygosity: a long homozygous run (or a coverage/mapping dropout) ends a block no matter how long the reads are. A genome is phased into MANY blocks, not one haplotype per chromosome, and between-block phase is arbitrary until a long-range method (trio, Hi-C) stitches them. So "the genome is phased" is meaningless without block N50 AND switch error together.

Tool Decision Tree

Switch-error accuracy is comparable across read-based tools (~0.1-0.4% on long reads); choose on speed, SV/mod co-phasing, platform, and pedigree.

| Scenario | Tool | Why | |----------|------|-----| | Careful default; indel phasing | WhatsHap (--reference --indels) | realignment mode rescues indels; widest downstream familiarity | | Parents/pedigree sequenced | WhatsHap --ped (PedMEC) | the gold standard - chromosome-scale, lowest switch error | | Whole-genome ONT speed | LongPhase (--ont) | ~10x faster; 30x human in ~1 min | | Co-phase SVs / methylation into long blocks | LongPhase (--sv-file/--mod-file) | a phased SV bridges het-sparse gaps; block N50 ~25 Mbp | | PacBio HiFi, joint small+SV+STR | HiPhase | PacBio-native one-pass phasing | | Multi-tech (Hi-C / 10x) | HapCUT2 | models Hi-C/linked-read error | | Inside PEPPER-Margin-DeepVariant | margin | legacy embedded haplotagger |

Clair3 uses WhatsHap (or LongPhase) internally to phase its het SNPs and haplotag the BAM feeding its full-alignment model - this skill owns that phase->haplotag mechanism (see clair3-variants).

The Tags (the central distinction)

| Layer | Tag | Meaning | |-------|-----|---------| | VCF (per variant) | GT with | vs / | 0|1 phased (order = which haplotype carries ALT); 0/1 unphased | | VCF (per variant) | FORMAT/PS (Integer) | phase-set / block id; variants sharing a PS are phased relative to each other (conventionally the first variant's position) | | BAM (per read) | HP:i:1 / HP:i:2 | the haplotype this read was assigned to (written by haplotag) | | BAM (per read) | PS:i:<int> | the phase set the read's assignment belongs to (matches the VCF PS) |

Unassigned reads carry NO HP tag (not HP:i:0). Do not confuse the VCF HP FORMAT tag (GATK style) with the BAM HP read tag.

Phasing Quality - Report Block N50 AND Switch Error

| Metric | Tool | Trap | |--------|------|------| | phase-block N50/NG50 | whatshap stats | contiguity, not correctness; gameable by over-joining blocks (which raises switch errors) | | phased fraction | whatshap stats | a tool can phase fewer easy sites to look better | | switch error rate | whatshap compare | the primary accuracy number | | switch vs flip decomposition | whatshap compare | a long switch propagates (damaging); a flip/short switch self-corrects (one wrong variant) - quote the decomposition | | Hamming distance | whatshap compare | hypersensitive to switch position (a switch near a block start flips half the block) |

Long blocks with a high switch rate are worse, not better, than honest short blocks. Benchmark against a trio-/strand-seq-phased GIAB truth.

Core Commands

# WhatsHap: phase (VCF), then haplotag (BAM). --reference enables realignment for indels.
whatshap phase -o phased.vcf.gz --reference ref.fa --indels variants.vcf.gz aln.bam
tabix -p vcf phased.vcf.gz
whatshap haplotag -o haplotagged.bam --reference ref.fa \
    --output-haplotag-list htlist.tsv.gz phased.vcf.gz aln.bam
samtools index haplotagged.bam

# Quality
whatshap stats --gtf blocks.gtf phased.vcf.gz                       # block N50, count, fraction
whatshap compare --names truth,mine truth.vcf.gz phased.vcf.gz      # switch error, flip decomposition

# Trio (gold standard) - --ped takes a PED file, not mother/father/child args
whatshap phase -o trio.vcf.gz --reference ref.fa --ped family.ped joint.vcf.gz mother.bam father.bam child.bam

# LongPhase: faster whole-genome, co-phase SNP+indel+SV(+5mC) into long blocks
longphase phase -s snps.vcf --indels --sv-file svs.vcf -b aln.bam -r ref.fa -o phased -t 16 --ont
longphase haplotag -s phased.vcf --sv-file phased_SV.vcf -b aln.bam -r ref.fa -o haplotagged -t 16

# Downstream consumer example: allele-specific methylation
modkit pileup haplotagged.bam asm/ --ref ref.fa --cpg --combine-strands --partition-tag HP

Per-Method Failure Modes

Phased VCF but no HP tags downstream

Trigger: running phase and pointing a read-level tool at the original BAM. Mechanism: phase writes the VCF only; the BAM HP tag comes from haplotag. Symptom: modkit returns only an ungrouped partition; IGV shows one color; Severus reports no phased SVs - all with no error. Fix: run haplotag; verify samtools view ... | grep HP:i:.

Short blocks blamed on the tool

Trigger: a homozygosity-rich or inbred sample phasing into many short blocks. Mechanism: no intervening hets to link across a long homozygous run - intrinsic, not tool failure. Symptom: low block N50 despite good reads. Fix: expect it; use ultra-long reads or co-phase SVs (LongPhase) to bridge sparse-het gaps; only trio/Hi-C makes it chromosome-scale.

Indels phased poorly

Trigger: whatshap phase without --reference. Mechanism: without realignment, allele support for indels in error-prone reads is noisy. Symptom: low indel phasing / errors. Fix: always pass --reference ref.fa (and --indels) on long reads.

Confident phasing of a haploid/CNV region

Trigger: phasing chrX/Y/MT in an XY sample, or inside a CNV/segdup. Mechanism: the two-haplotype model is false there (hemizygous, >2 or 1 haplotype, or collapsed paralogs). Symptom: spurious micro-blocks, HP counts far from 50/50. Fix: treat phasing there as unreliable; do not interpret it as biology.

Quoting N50 alone

Trigger: comparing phasers on block N50. Mechanism: N50 is inflated by over-joining, which raises switch errors. Symptom: "longer blocks" that are actually worse. Fix: report block N50 AND switch error together; use the flip decomposition.

Quantitative Thresholds

| Threshold | Source | Rationale | |-----------|--------|-----------| | Total depth ~15-20x for confident phasing | phasing practice | per-haplotype depth is ~half; below ~10x blocks fragment | | --max-coverage 15 is a runtime cap | WhatsHap | wMEC is exponential in per-site coverage; >15x is redundant, not required | | long-read switch error ~0.1-0.4% | benchmarks vs trio truth | the achievable accuracy band | | LongPhase SNP+SV block N50 ~25 Mbp | Lin 2022 | co-phasing SVs bridges het-sparse gaps (vs ~10-15 Mbp SNP-only) | | ASM wants ~20x total | methylation practice | each haplotype must clear the ~10x per-site floor |

Common Errors

| Error / symptom | Cause | Solution | |-----------------|-------|----------| | modkit --partition-tag HP has only an ungrouped partition | BAM never haplotagged | run whatshap haplotag / longphase haplotag | | --trio flag not recognized | the flag is --ped | pass a PED file: --ped family.ped | | Poor indel phasing | --reference omitted | add --reference ref.fa --indels | | 0 reads usable in phase | BAM @RG sample != VCF sample | --ignore-read-groups (or fix sample names) | | longphase --platform ont errors | platform is a bare flag | use --ont or --pb | | Spurious phasing on chrX/CNV | diploid assumption violated | treat as unreliable; exclude haploid/CNV regions |

References

• Patterson M, Marschall T, Pisanti N, et al. 2015. WhatsHap: weighted haplotype assembly for future-generation sequencing reads. J Comput Biol 22(6):498-509.
• Martin M, Patterson M, Garg S, et al. 2016. WhatsHap: fast and accurate read-based phasing. bioRxiv 085050.
• Garg S, Martin M, Marschall T. 2016. Read-based phasing of related individuals (PedMEC). Bioinformatics 32(12):i234-i242.
• Lin JH, Chen LC, Yu SC, Huang YT. 2022. LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants. Bioinformatics 38(7):1816-1822.
• Holt JM, Saunders CT, Rowell WJ, et al. 2024. HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics 40(2):btae042.
• Edge P, Bafna V, Bansal V. 2017. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res 27(5):801-812.

Related Skills

• clair3-variants - Produces the het VCF; Clair3 phases+haplotags internally via this mechanism
• long-read-alignment - Produces the BAM (keep -Y so supplementaries are taggable)
• nanopore-methylation - Allele-specific methylation via modkit --partition-tag HP
• structural-variants - Severus consumes a haplotagged BAM for phased/somatic SVs
• basecalling - LongPhase can co-phase 5mC from a modBAM
• phasing-imputation/haplotype-phasing - Statistical/reference-panel phasing for imputation
• genome-assembly/hifi-assembly - Phased de novo haplotype contigs (trio/Hi-C)
• hi-c-analysis/contact-pairs - Hi-C long-range phasing (orthogonal)