FindNullomerVariants

Removes nullomers that are likely to result from common variants in a user specified variant VCF file.

Required arguments:

Argument	Explanation
–population_variants_input_filepath	Path to the input variant file containing common population variants.
–nullomer_mutations_input_filepath	Path to the input variant file containing mutations that cause neomers.
–population_variants_output_filepath	Path of the output file containing neomer-causing population variants.
–non_population_variants_output_filepath	Path of the output file containing nullomer-causing non-population variants.

Optional arguments:

Argument	Explanation
–chr_col	Column number of input variant file indicating the variant chromosome (Default=0, for .vcf format)
–pos_col	Column number of input variant file indicating the variant position (Default=1, for .vcf format)
–ref_col	Column number of input variant file indicating the reference allele (Default=3, for .vcf format)
–alt_col	Column number of input variant file indicating the alternative allele (Default=4, for .vcf format)
–freq_col	Column number of input population variant file indicating frequency of the alternative allele (MAF) (Default=5)

Outputs:

• VCF-compatible file containing all variants from nullomer_mutations_input_filepath that do not contain a common popoulation variant.