Errors without BED file

[adammaikai]

Is there a way to perform realignment without the use of a BED file, for example, in WGS cases?
Thank you.

[mozack]

Currently, a bed file is always required. A workaround is to simply specify all chromosomes with a range of 1 to chromosome length in the bed file. For example, for HPV we use:
NC_001357.1 1 7857
NC_001526.2 1 7905

ABRA does not currently scale well to human WGS. For our very limited WGS testing we split up BAM files by chromosome and ran ABRA on each independently. Unfortunately, even that does not scale well - WGS has simply not been a common use case for us to date.