VCF Record Audit

Audit VCF record field count and essential fields for the supplied number of samples.

Description

VCF records store variant fields separated by tabs.

VCF records store variant fields separated by tabs. Sample-free records have eight columns; sample records add FORMAT and one column for each sample.

Audit VCF record field count and essential fields for the supplied number of samples.

When to use VCF Record Audit

Use this for the following task: Audit VCF record field count and essential fields for the supplied number of samples.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use VCF Record Audit and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter record, expectedSampleCount using the field table, then run the tool.
Read columnCount, valid, issues. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
record	Record	string	Required
expectedSampleCount	Expected sample count	integer	Required

Trim trailing whitespace, split tabs, then audit column count, chromosome, positive integer POS, reference bases, alternate presence and nonempty FORMAT when samples exist. Return issue names with valid.^[1]

expected columns = 8 without samples, otherwise 9 + sampleCount

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
columnCount	Column count	integer
valid	Valid	boolean
issues	Issues	list of string

json

{
  "input": {
    "record": "chr1\t100\t.\tA\tG\t30\tPASS\t.\tGT\t0/1",
    "expectedSampleCount": 1
  },
  "output": {
    "columnCount": 10,
    "valid": true,
    "issues": []
  }
}

Limitations and assumptions

This is an essential-field audit, not full VCF conformance. INFO, genotype content and detailed ALT syntax are not validated.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose VCF Header Audit for this operation: Audit VCF fileformat, column header, optional contig declarations, and sample identifiers. For a complementary task, use Trio Mendelian Check for this operation: Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

VCF Record Audit — tool.io

Similar or alternative tools

VCF Header Audit
Audit VCF fileformat, column header, optional contig declarations, and sample identifiers.
Trio Mendelian Check
Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.