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mavis/convert/straglr

convert_row()

Converts the fields from the original STRAGLR BED output into MAVIS definitions of an SV Since STRAGLR defines regions where short tandem repeats exist we make the definitions here fairly non-specific

See their github page for more details: https://github.com/bcgsc/straglr

BED Columns - chrom: chromosome name - start: start coordinate of locus - end: end coordinate of locus - repeat_unit: repeat motif - allele.size: where N={1,2,3...} depending on --max_num_clusters e.g. N={1,2} if --max_num_clusters==2 (default) - allele.copy_number - allele.support

def convert_row(row: Dict) -> Dict:

Args

  • row (Dict)

Returns

  • Dict