Parses vcf files to reformat/add INFO fields and metaData headers and/or select entries belonging to a subgroup e.g. a list of genes. Input can be piped or supplied as an infile.

Usage infile.vcf > outfile.vcf infile.vcf --parseVEP 1 -rf External_Db.txt -rf_ac 3 -sf genes.v1.0.txt -sf_mc 3 -sf_ac 3,4,11,15,17,20 -sof selected_genes.vcf > outfile.vcf


vcfParser is written in Perl, so naturally you need to have Perl installed. The perl module Set::IntervalTree is required and are used to add “ranged” annotations.


Parses the output from VEP to include RefSeq transcripts. The transcript and protein annotations, moste severe consequence and gene annotations are also included in the output . Transcript protein predictions (Sift and Polyphen) can also be included.

Select Mode

A list of genes and their corresponding HGNC Symbol can be used to fork the analysis into “selected” genes and “orphan” genes.

GuideLines on format for database of genes

  • The database file should contain a header line starting with “#”.
  • The number of headers should match the number of field elements for each entry.
  • Do not use whitespace in headers.
  • Do not use ”;” in file.
  • Separate elements in fields with ”,”. Do not use ”, ”.
  • No whitespace in the beginning or end within fields.
  • No entries should be duplicated within database.
  • Length of gene coordinates should be greater than 0
  • Only digits in gene coordinate entries

Range Annotations

vcfParser can also add range annotations to the vcf by using the Set::IntervalTree perl cpan module and a file with chromosomal coordinates and features to be annotated.