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parses the alt statement from vcf files using the specification in vcf 4.2/4.2.

Assumes that the reference base is always the outermost base (this is based on the spec and also manta results as the spec was missing some cases)

r = reference base/seq u = untemplated sequence/alternate sequence p = chromosome:position

alt format orients
ru[p[ LR
[p[ur RR
]p]ur RL
ru]p] LL
def parse_bnd_alt(alt):


  • alt

converts a vcf record

def convert_record(record, record_mapping={}, log=DEVNULL):


  • record
  • record_mapping
  • log


CT = connection type, If given this field will be used in determining the orientation at the breakpoints. From!topic/delly-users/6Mq2juBraRY, we can expect certain CT types for certain event types - translocation/inverted translocation: 3to3, 3to5, 5to3, 5to5 - inversion: 3to3, 5to5 - deletion: 3to5 - duplication: 5to3

process a VCF file

def convert_file(input_file: str, file_type: str, log):


  • input_file (str): the input file name
  • file_type (str): the input type
  • log


  • err: [description]