opengenomics/tcgavcf-tool repository overview

⁠tcga-vcf-reheader-tool

Tool to read a TCGA Variant Call Format (VCF) file and output an equivalent file with a different header

⁠Requirements

• Python 2.7
• PyYAML

⁠Usage

tcga-vcf-reheader.py input_file_path output_file_path parameter_file_path

• input_file_path: the VCF to read
• output_file_path: the VCF to write
• parameter_file_path: a YAML file describing the additions/changes to the header

Currently only changes to the ##SAMPLE lines are supported. Any existing ##SAMPLE lines will be replaced by the ones specified in the YAML file.

WARNING: This tool will completely replace any existing ##SAMPLE lines. If the parameter file names different samples than were used in the VCF, the resulting output will be a misleading chimeric monster.

⁠Contributors

• Kyle Ellrott [email protected]⁠
• Walker Hale [email protected]⁠
• Dave Larson [email protected]⁠
• Lee Lichtenstein [email protected]⁠

⁠tcgavcf-tool