variant tools uses file format specification files (.fmt) files to describe file formats so that commands such as vtools import, vtools update and vtools export know how to import data from and export data to files in such formats.

  • variant tools can import variants, variant info fields, genotypes, and genotype info fields from a file. The file must contain information about variants (chr, pos, ref, alt), although variant tools is able to obtain information from other sources if some of the variant info fields are missing. (For example, variant tools can retrieve reference alleles from a reference genome).
  • variant tools can update variant info fields and genotype info fields for existing variants and genotypes. The file can be variant-based (contains chr, pos, ref and alt), position-based (contains chr and pos), and range-based (contains chr, starting and ending positions). In the latter cases, a record in the input file can update multiple variants at the specified location or range.
  • variant tools can export variants, variant info fields, genotypes, and genotype info fields to a file. The format description file must define columns, which specify what and in which format to export to each column of the output file.

variant tools can import and export data in the following formats. We try to update descriptions of these formats as soon as possible but please use commands such as

% vtools show formats
% vtools show format basic

to get the most updated information about these formats.

NameImportUpdateExportComment
basicY YImport variants in tab-delimited format, export variants and optional variant info fields and genotypes
VCFYYYVariant Call Format (VCF version 4.0 and 4.1)
CSVY Ycsv format
ANNOVAR  YFormat of ANNOVAR input file.
ANNOVAR_variant_functionY  used to imported annotations from ANNOVAR *.variant_function files.
ANNOVAR_exonic_variant_functionY  imports annotations from files generated from ANNOVAR of the form *.exonic_variant_function.
CASAVA18_snpsY  Illumina snps.txt format
CASAVA18_indelsY  indels.txt from Illumina
CGAY  Complete Genomics CGA masterVarBeta$ID.tsv.bz2 file
Pileup_indelY  Pileup Indel format
MAPY  Import variants from files with only chr and pos information. reference and alternative alleles are retrieved from dbSNP.
PLINKYY Import variants and sample genotypes from PLINK file format. Currently only PLINK binary file input is supported.
Polyphen2?Y YExport data in Polyphen2 batch query, import information from results returned by the polyphen2 batch query server.
TPED?  Y 
twoalleles?Y  Import alleles as allele 1 and 2, use a reference genome to determine which one is reference
rsnameY  Import variants from rsnames, using the dbSNP database to query variants

Customize import/export format: