Tool:simplify the output of a vcf file using vcf_simplify-v1.py
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3.3 years ago
kirannbishwa01 ★ 1.3k

There exits several tools that help mine, filter and manipulate the data from VCF file. I still felt that there was a tool missing that can simplify the data represented in the VCF input file to a table file. Most of the VCF simplification are for more population tags, fields and one sample per VCF.

vcf_simplify.py https://github.com/everestial/vcf_simplify , is a python3 parser that helps simplify the data representation of any type of fields from INFO and FORMAT of every SAMPLE of interest. This tool is written in python3 with cyvcf2 https://github.com/brentp/cyvcf2/ , so it is considerably faster than pyVCF module.

Hope you like it.

vcf table python variants Tool • 774 views