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weizhouUMICH / SAIGE

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Error Step 2: The number of samples specified in the sample file does not equal to the number of samples in the bgen file #384

Closed Mahmedturk closed 2 years ago

Mahmedturk commented 2 years ago

Hi, This is my first time doing the RSAIGE analyses, kindly excuse me if it's a basic question. After doing successfully step 1 on chromosome 22 i get the below error on step 2. Any help would be greatly appreciated.

Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, : ERROR! The number of samples specified in the sample file does not equal to the number of samples in the bgen file Execution halted

weizhouUMICH commented 2 years ago

Hi @Mahmedturk, The sample file contains one column without any header for all sample IDs that match the order in the bgen file. Can you have a check?

Thanks, Wei

weizhouUMICH commented 2 years ago

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. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei