Comments (6)
dajiangliu
commented on June 7, 2024
Did you try --meta score option? --single score is less actively maintained for now.
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jielab
commented on June 7, 2024
still got the same error. I think the segmentation fault error came from reading the input file, RVTESTS has not gone to --meta or --single part yet. I still don't understand why the log file says "from VCF files" even when i specify it to read a .bgen file. And i don't know where to specify the .sample file.
BTW, I used PLINK2a to read this .bgen file, and there is no problem.
best regards,
Jie
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zhanxw
commented on June 7, 2024
Hi Jie,
I will look into this issue.
Our initial goal is to use bgen files as genotype inputs and ped files as phenotype inputs. I will see how to incorporate .sample file.
Xiaowei
… On Sep 13, 2017, at 10:01 PM, jiehuang001 ***@***.***> wrote:
still got the same error. I think the segmentation fault error came from reading the input file, RVTESTS has not gone to --meta or --single part yet. I still don't understand why the log file says "from VCF files" even when i specify it to read a .bgen file. And i don't know where to specify the .sample file.
BTW, I used PLINK2a to read this .bgen file, and there is no problem.
best regards,
Jie
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zhanxw
commented on June 7, 2024
The current version of RVTESTS requires that .bgen file includes sample names. In that case a separate .sample file is not be needed. I just learned that many other .bgen files do not include sample names. In that case, I need to make RVTESTS support loading .sample file.
I will work that, and update this issue.
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jielab
commented on June 7, 2024
I see. i will not use RVTESTS for .bgen files based association analyses, for now then. Hopefully you will release a new version soon that address the issues that I raised.
Best regards,
Jie
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zhanxw
commented on June 7, 2024
@jiehuang001 This version (https://github.com/zhanxw/rvtests/releases/tag/v2.0.6) should support BGEN format. Please let me know if you have additional questions. Thanks.
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Related Issues (20)
- Job run time
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