search

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
187 stars 72 forks source link

Open VCF failed #368

Closed lgb-cyber closed 2 years ago

lgb-cyber commented 2 years ago

Hello, I am running the step2_SPAtests.R. However, it reported error : Open VCF failed and the step2 stopped. image This is what my VCF file looks like, is there anything wrong ? image looking forward to answer, thanks!

huiyee1 commented 2 years ago

Hi, I encounter the same issue. Did you find any solution?

huiyee1 commented 2 years ago

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.

liwangchang commented 2 years ago

@huiyee1 Still unable to solve the problem, I asked for help

weizhouUMICH commented 2 years ago

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