liftover hg19 to hg38 fragmented

Question

[heureuse]

Good morning, I performed a liftover from hg19 to hg38. The result is fragmented. I had 91 lines in hg19 and I end up with 7003 in hg38. I have a script to do the merge in 1 nucleotide steps but I'm not sure if that's what to do. Has anyone been in this situation before?

Thank you

[Pierre Lindenbaum]

I have a script to do the merge in 1 nucleotide steps

it's not clear. What's the input ? what are the duplicated lines ? what's the script ? don't you fall in multiple-mapped areas ?

[heureuse]

I use crossmap.py to do my liftover. The input is a bed file hg19 and the chain file (hg19 to hg38). The lines are not duplicated but fragmented. For example for one entry in hg19, I have 6 entry in the lifted file