vcf2tsv command can be used to convert a VCF to a tab-delimited file.
Converts a VCF into a tsv - in wide or long format, and taking into account annotation fields (ANN) added by programs such as SNPeff.
usage: vk vcf2tsv (wide|long) [--print-header --ANN] <vcf>
- wide | long - Select one of wide or long to set the output format.
- --print-header - Print a header row specifying column names.
--ANN - Parse annotation fields. Results in 1 row x (n)annotations x (n)samples when long or 1 row x (n)annotations x (n)variants when wide.
wide- Prints a row for every CHROM:POS x # annotations (if
--ANNis specified). A row will be output for every annotation.
long- Prints a row for every CHROM:POS x sample x annotation (if
--ANNis specified) combination.
For example, if a SNP at CHROM=II, POS=100 has two annotations and five samples, there will be (CHROM:POS) x (annotations) x (samples) = 10 lines output.
--ANN - Expands ANN fields added by variant prediction programs (e.g. SnpEff). When multiple annotations are present, a row is output for each annotation. This is for both wide and long format.