Closed lgb-cyber closed 2 years ago
Hi, I encounter the same issue. Did you find any solution?
Hi, @lgb-cyber I just found out that the problem solved by adding the option: --chrom You need to define which chromosom. For example, --chrom 1 for chromosome 1.
@huiyee1 Still unable to solve the problem, I asked for help
Sorry for the very late reply! We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.
Thanks! Wei
Hello, I am running the step2_SPAtests.R. However, it reported error : Open VCF failed and the step2 stopped.
This is what my VCF file looks like, is there anything wrong ?
looking forward to answer, thanks!