Description
Hello,
I have a .hal file that was created with cactus and then used halBranchMutations to identify insertions, deletions and SNPs along the tree.
As output I received bed files. I then wanted to use halLiftover to have the coordinates based on the same target for each genome including the ancestors. I used the bed files received by halBranchMutations and the same .hal file as input.
However, I get the following error: "hal exception caught: Error converting string to int: Start in input bed line 1"
I also tried to delete the header but this did not help either. Also adding the option --bedType did not remove the error. To me everything in the column start looks convertable to integer.
I attach an example of a bed file used as input.
test.txt
I installed cactus v2.8.1 and am using the hal tools through that. The version of halLiftOver is v2.2
Do I need to change the .bed file received as output from halBranchMutations in a certain way or should this theoretically be compatible?
Thanks,
Michaela