variant_call_summary
Read-only
Summarize a variant call set the way bcftools stats does: records by class, transitions and transversions with their ratio, the twelve directed substitutions, indel lengths, per-contig counts, the FILTER tally, the QUAL range, and per-sample genotype counts. Reports what could NOT be counted rather than leaving a zero standing in for it, meaning a file whose genotypes were not parsed, and any genotype naming an allele its record never declares.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file | No | which call set in this project, by name. Unset, it is the project's only one, and it refuses rather than guessing when there is more than one. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| contig | No | summarize ONE contig instead of the whole file, named as the file names it. The per-contig table is always over everything read; this narrows what everything else counts. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| pass_only | No | count only records whose FILTER is PASS or unset. A Ts/Tv computed over unfiltered calls and one computed over passing calls are different measurements, and this is which one you asked for. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| qual | Yes | min, max, median and the number of records stating no QUAL. Null when nothing stated one, which is not the same as a range of zero | |
| tstv | Yes | ts, tv and ratio over every ALT, and tsFirstAlt/tvFirstAlt/ratioFirstAlt over each site’s first ALT only. Both, because bcftools reports both and a multiallelic call set makes them differ | |
| counts | Yes | records, samples, and the class tallies: snps, mnps, indels, others, noAlts, multiallelicSites and multiallelicSnpSites. A site counts in every class its alleles carry, which is how bcftools counts them | |
| filters | Yes | every FILTER value seen with its count, including PASS and the unfiltered (`.`) tally: the two are different states and are counted apart | |
| summary | Yes | the call set in one sentence, generated from this run | |
| indelPlot | Yes | sites per indel length (ALT minus REF), deletions left of zero and insertions right of it | |
| per_contig | Yes | records, snps and indels per contig, over everything read | |
| per_sample | Yes | bcftools' PSC section per sample: refHom, nonRefHom, hets, transitions, transversions, indels, averageDepth, singletons, hapRef, hapAlt and missing | |
| not_counted | Yes | what this run could NOT count and why: `genotypesUnavailable` when the file's genotypes were not parsed (so per_sample is empty for a reason), and `badAlleleCalls` listing genotypes naming an allele their record never declares. Real bcftools stats exits on such a file rather than reporting per-sample numbers, so a non-empty list means per_sample has no bcftools counterpart to be compared against | |
| indel_lengths | Yes | indel length (ALT minus REF) to the number of sites, sorted by length: bcftools' IDD section. Negative is a deletion | |
| substitutions | Yes | the twelve directed substitution types with their counts | |
| substitutionMap | Yes | the twelve directed substitutions as a REF by ALT grid, the Summary tab’s bars as one picture; the diagonal is empty, since a base does not substitute for itself |