ExtractMutationNullomers

Finds all mutations that cause the resurfacing of a list of nullomers.

Required arguments:

Argument	Explanation
–genome_filepath	Path to the fasta file containing the genome being analyzed.*
–nullomer_input_filepath	Path to the .txt file containing the nullomers absent from the supplied genome.
–mutation_input_filepath	Path to the file containing variants to be analyzed.
–mutation_output_filepath	Path to the output file where the neomer-causing mutations will be written to.
–nullomer_length	Length of nullomers being analyzed.

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)

Outputs:

• VCF-compatible file containing variants from provided variant file that cause at least one nullomer to resurface.

Note

^* This file must be formatted such that the FASTA headers read “>chr1”, “>chr2”, “>chr3”, …