Convert VCF Variants to TSV

About this tool

VCF files are compact for variant callers, but awkward in spreadsheets: the fixed columns are followed by semicolon-delimited INFO annotations and, often, colon-delimited FORMAT values for each sample. This tool turns those records into tidy TSV so you can inspect, filter, or join variants with ordinary table tools.

The output always starts with CHROM, POS, ID, REF, ALT, QUAL, and FILTER. When enabled, INFO fields are expanded into one column per key. Sample FORMAT values can be written in long layout (one row per variant × sample with a SAMPLE column) or wide layout (one row per variant with columns such as NA001_GT and NA001_DP).

Worked example

Paste this VCF:

##fileformat=VCFv4.2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA001	NA002
chr1	100	rs1	A	G	50	PASS	DP=30;AF=0.5	GT:DP	0/1:20	1/1:10

With the default long layout, the TSV contains two data rows, one for NA001 and one for NA002, with INFO columns DP and AF plus FORMAT columns GT and DP.

Controls

• Sample layout chooses long rows for sample-centric analysis or wide rows for variant-centric spreadsheets.
• Explode INFO fields adds one column per INFO key; use INFO keys to keep such as DP,AF,AC when you only need selected annotations.
• Include sample FORMAT fields emits genotype/sample values when the VCF has sample columns.
• PASS-only drops filtered calls and keeps records whose FILTER is PASS or ..
• Prefix INFO columns writes INFO_DP instead of DP, useful when INFO and FORMAT have the same key.
• Missing value controls the placeholder for absent INFO/FORMAT/sample values.

Limits and edge cases

This is a table flattener, not a genomic normalizer. It does not split multi-allelic ALT values, left-align variants, query reference FASTA files, parse compressed .vcf.gz, or validate VEP/ANN subfield semantics. Convert compressed files to text first and paste a representative VCF section. Values are made TSV-safe by replacing embedded tabs/newlines with spaces.

FAQ