You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: