pyvcf2tsv: genomic VCF to tab-separated values (TSV)

 

A small Python program that converts genomic variant data encoded in VCF format into a tab-separated values (TSV) file.

The program utilizes the cyvcf2 library to parse the VCF file. By default, the program prints the fixed VCF columns, all INFO tag values (as defined in the VCF header, INFO tags not present in a given record is appended with a '.'), and all genotype data (FORMAT columns) for heterozygotes and homozygotes. If genotype data is present, it prints one line per sample, and a column denoted VCF_SAMPLE_ID indicates data for a given sample. Importantly, the program has optional arguments to

• skip sample genotype data (i.e. FORMAT colums) - print only variant information
• keep rejected genotypes (i.e. FILTER != 'PASS' / GT == './.')
• skip INFO data.
• compress output TSV
• print data types of VCF columns as a header line

IMPORTANT: If you run pyvcf2tsv with a large multi-sample VCF file, the file size of the output TSV will quickly grow fairly large, since there is, by default, one line per sample genotype in the output. Turn on --skip_genotype_data if you are primarily interested in the variant INFO elements, file size of output TSV will also be considerably smaller.

News

• March 9th 2023: 0.6.1 release
  • Handling of cases where a tag is found both in INFO and FORMAT columns of VCF (e.g. DP). For such cases, the INFO tag name is now prepended with a INFO_ string (e.g. INFO_DP), ensuring non-duplicate columns in the final output TSV file.

Installation

The software can be installed with the Conda package manager, using the following command:

conda install -c bioconda pyvcf2tsv

Usage

pyvcf2tsv --input_vcf <INPUT_VCF> --out_tsv <OUTPUT_TSV>
       -h [options]

pyvcf2tsv:  Convert a VCF (Variant Call Format) file with genomic variants to a file with
        tab-separated values (TSV). One entry (TSV line) per sample genotype.

Required arguments:
    --input_vcf INPUT_VCF   Bgzipped input VCF file with input variants (SNVs/InDels)
    --out_tsv OUT_TSV       Output TSV file with one line per non-rejected sample genotype
                        (variant, genotype and annotation data as tab-separated values)

Optional arguments:
    --skip_info_data        Skip output of data in INFO column
    --skip_genotype_data    Skip output of genotype_data (FORMAT columns)
    --keep_rejected_calls   Output data also for rejected (non-PASS) calls
    --print_data_type_header    Output a header line with data types of VCF annotations
    --compress              Compress output TSV file with gzip
    --version               Show program's version number and exit