molamola --vcf VCF [--out DIR] [--reference hg38|t2t] [...]
Single flat parser: the plot type is auto-detected from the VCF header. ##INFO=<ID=SVTYPE,...> selects the SV / cytogenetics report; ##INFO=<ID=CSQ,...> AND ##FORMAT=<ID=PS,...> selects the per-gene compound-het panels. Mode-specific flags are silently ignored when they don’t apply to the detected mode (e.g. passing --gene against an SV VCF — the SV mode just doesn’t read it).
VCFs that match neither shape are refused with a clear error rather than rendering a misleading default.
See FILTERS.md for what every threshold does. See OUTPUTS.md for the output format.
| flag | default | description |
|---|---|---|
--vcf PATH |
required | input VCF (gzipped OK). |
--out DIR |
parent of --vcf |
output directory. The report <sample>.report.html (SV) or <sample>.compound_het.report.html (compound-het) is written here. |
--reference {hg38,t2t} |
hg38 |
reference assembly the input VCF was called against. SV mode supports both; compound-het mode is hg38-only (the bundled canonical-exon and ClinVar refs are hg38-coordinate). |
--sample NAME |
VCF basename | sample label shown in the report header. |
--force |
off | bypass the safety check that errors out when the VCF filename hints at a reference different from --reference (e.g. sample.t2t.vcf with --reference hg38). |
Active when the input VCF carries ##INFO=<ID=SVTYPE,...> (Sniffles2 / cuteSV / SVIM / pbsv / NanoVar).
| flag | default | description |
|---|---|---|
--filter {pass,all} |
pass |
keep PASS BNDs only, or include GT-filtered events. |
--caller {auto,sniffles2,sniffles1,cutesv,svim,pbsv,nanovar} |
auto |
SV caller; auto runs an INFO-fingerprint detector and falls back to sniffles2 on no match. Override useful for bcftools-merged or re-headered VCFs. |
--mark-acrocentric / --no-mark-acrocentric |
on for hg38, off for t2t | grey out BNDs with both ends in chr13/14/15/21/22 p-arms (mostly mapping artefacts on hg38; real sequence on T2T-CHM13v2.0). |
--cov-filter {none,mark,drop} |
mark |
how to handle coverage-spike BNDs and DEL/DUP. mark greys flagged BNDs and drops noisy DEL/DUP from density strips; drop also removes flagged BNDs entirely; none ignores. |
--cov-ratio R |
auto |
max(COVERAGE) / baseline threshold above which an event is suspicious. Default auto = max(2.0, p99 of in-sample distribution) per sample. The chosen value is printed at run start. |
--cov-vaf-max V |
0.35 |
VAF below which a high-coverage event is treated as repeat-collapse noise. |
--focus CHR:POS |
none | show only BNDs with an endpoint within --focus-window of CHR:POS. The second part can be either a position (chr7:57716411) or an ISCN cytoband (chr7:q11.23). Repeatable. |
--focus-window N |
1000 |
+/-bp tolerance for --focus matching. |
--min-svlen N |
50 |
hard SVLEN cutoff (bp) for non-BND SVs. Set 0 to disable. BNDs are unaffected. |
--bin-size N |
1,000,000 |
density-track bin width in bp. |
Active when the input VCF carries ##INFO=<ID=CSQ,...> AND ##FORMAT=<ID=PS,...> (phased + VEP-annotated small-variant VCF).
| flag | default | description |
|---|---|---|
--gene SYMBOL |
none | plot exactly this gene; repeatable. Plots regardless of variant count (with a clear placeholder for empty cases). When omitted, the auto-select rule picks candidate genes. |
--clinvar PATH |
bundled | override the bundled ClinVar lookup. Accepts either molamola’s reduced TSV (default at data/clinvar.hg38.tsv.xz) or NCBI’s raw ClinVar VCF. Format auto-detected by .tsv vs .vcf extension. |
--canonical-exons PATH |
bundled | override the bundled canonical-exon TSV (default: data/canonical_exons.hg38.tsv.gz). |
--min-pair-count N |
1 |
auto-select threshold: gene qualifies iff at least one phase set has >= N trans pairs where one anchor is ClinVar P/LP or VUS and the partner is not benign. The HTML splits results into a strict section (both P/LP or VUS) and an extended section (anchor P/LP-or-VUS, partner conflicting / no-ClinVar / P/LP / VUS). Ignored when --gene is given. |
--max-genes N |
50 |
cap on the number of auto-selected genes; capped runs emit a stderr warning. |