vcf2tsvpy | Genomic VCF to tab-separated values

vcf2tsvpy is a Python library. vcf2tsvpy has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

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. IMPORTANT: If you run vcf2tsvpy 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.