BEDPE format specification

[pacitti]

can you please post the link to the BEDPE format specification that INTEGRATE-Neo requires? the fusions.bedpe and result.bedpe example files you provide are in formats different from this BEDPE format documentation at bedtools: https://bedtools.readthedocs.io/en/latest/content/general-usage.html. I haven't been able to locate the BEDPE format specification at dreamchallenges.org.

your prompt response is greatly appreciated.

Thank you.

[mjinkm]

Hi pacitti,

Fields 1-10 of the input (in the examples, fusions.bedpe) and output (in the examples, result.bedpe) BEDPE files are as described in the BEDPE format documentation at bedtools. The 11th field of each is the number of spanning reads which INTEGRATE-fusion found supporting the fusion. Fields 12-19 of the output BEDPE are as described in the "output" section of the ReadMe:
Epitope sequence
Epitope Affinity (nanoMolar)
HLA allele
HLA category
HLA score
HLA e-value
HLA confidence