Tool to read a TCGA Variant Call Format (VCF) file and output an equivalent file with a different header
- Python 2.7
- PyYAML
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.
- Kyle Ellrott kellrott@soe.ucsc.edu
- Walker Hale hale@bcm.edu
- Dave Larson dlarson@genome.wustl.edu
- Lee Lichtenstein lichtens@broadinstitute.org