I would like to use VarSim to generate synthetic reads for structural variants from a given ground truth VCF file. To achieve this, I am using VarSim with the following parameters:
However, this command raises the following error:
ValueError: Need SV sequence file to fill in SV sequences
I think this error is because of missing --sv_insert_seq parameter. From the documentation, I can see that this argument is a file that contains the sequences to be inserted into the reads. I am wondering why this argument is required when a VCF file is provided to create the SVs from.
Hello,
I would like to use VarSim to generate synthetic reads for structural variants from a given ground truth VCF file. To achieve this, I am using VarSim with the following parameters:
However, this command raises the following error:
ValueError: Need SV sequence file to fill in SV sequences
I think this error is because of missing
--sv_insert_seq
parameter. From the documentation, I can see that this argument is a file that contains the sequences to be inserted into the reads. I am wondering why this argument is required when a VCF file is provided to create the SVs from.