Liftover Error: Start Coordinate Is After End Coordinate

Question

[Aishwarya Kulkarni]

After running the lifover, I am getting an error

Reading liftover chains
Mapping coordinates
ERROR: start coordinate is after end coordinate (chromStart > chromEnd) on line 1 of bed file ABCD.bed
ERROR: chr8 94747805 94747070

There are many such rows in the bed, what would be the best option of dealing with such rows?

Switching the positions or eliminating such rows and why?

Thanks

[Ashutosh Pandey]

Just switch the positions if end < start.

Answer 1

[Istvan Albert]

Your input file has an incorrect format.