VCF Header Audit
Audit VCF fileformat, column header, optional contig declarations, and sample identifiers.
Description
VCF headers describe the format and record columns before variant data.
VCF headers describe the format and record columns before variant data. Sample identifiers and optional contig declarations help consumers interpret records consistently.
Audit VCF fileformat, column header, optional contig declarations, and sample identifiers.
When to use VCF Header Audit
Use this for the following task: Audit VCF fileformat, column header, optional contig declarations, and sample identifiers.
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 Header 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 header, requireContigDefinitions using the field table, then run the tool.
- Read valid, issues, sampleNames. 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 |
|---|---|---|---|
| header | Header | string | Required |
| requireContigDefinitions | Require contig definitions | boolean | Required |
Ignore empty CRLF/LF lines. Require first nonempty line to name VCFv4.x, exactly one #CHROM header with standard columns and FORMAT when samples exist, and distinct nonempty sample IDs. Check contig declaration presence only when requested.1
valid = no fileformat-first, columns, contig-definitions or sample-identifiers issues This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| valid | Valid | boolean |
| issues | Issues | list of string |
| sampleNames | Sample names | list of string |
{
"input": {
"header": "##fileformat=VCFv4.3\n##contig=<ID=chr1>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n",
"requireContigDefinitions": true
},
"output": {
"valid": true,
"issues": [],
"sampleNames": []
}
}Limitations and assumptions
The check does not validate metadata declaration bodies or constrain x to a published minor version.
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 Record Audit for this operation: Audit VCF record field count and essential fields for the supplied number of samples. For a complementary task, use FASTA Line Width Audit for this operation: Audit wrapping of nucleotide or protein FASTA records at a caller-supplied width, allowing a shorter final sequence line.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
VCF Header Audit — tool.io
Similar or alternative tools
- VCF Record Audit
Audit VCF record field count and essential fields for the supplied number of samples.
- FASTA Line Width Audit
Audit wrapping of nucleotide or protein FASTA records at a caller-supplied width, allowing a shorter final sequence line.