Do bam files need to be sorted /indexed before input to BRAKER2?

Open krabapple opened this issue 6 years ago • 2 comments

The BRAKER manual does not specify. I'm using STAR as the aligner. The Augustus protocol paper (Hoff and Stanke 2018) calls sorting optional (if using the STAR aligner).

Jan 22 '20 20:01 krabapple

BRAKER does not sort the bam file if bam2hints is called, only. It will sort the bam file prior converting it to a wiggle file in case of UTR training.

Feb 20 '20 20:02 KatharinaHoff

Does that mean it sorts the input bam file when --UTR , --addUTR, or either, are used?

It also means that a file used in a --bam= option never needs to be sorted before running the BRAKER command?

May 05 '21 20:05 krabapple