I am trying to use bedtools getfasta on some bed files, but the issue is that the peaks bed file columns are mixed up such that the first column with the chromosome names contains the peak location as well for some of the chromosomes. How can I reorganize the bed file so that the chromosome names are separated from the peak locations and etc.
This is an output I received while running the bedtools getfasta command.
Feature (3R:7071004-7071004) has length = 0, Skipping. Feature (3R:7072290-7072290) has length = 0, Skipping. Feature (3R:3298414-3298414) has length = 0, Skipping.