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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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How many `--extract` are allowed in Regenie step 2? #119

Closed Shicheng-Guo closed 3 years ago

Shicheng-Guo commented 3 years ago

regenie allow two --extract or not? I want to use two --extract to select SNPs to be used in the analysis.

For example, the first --extract use to select INFO score>0.8 and second extract to select MAC>=5

Thanks.

Shicheng

joellembatchou commented 3 years ago

Hi Shicheng,

Regenie does not allow mutilple extract files. You could easily bypass that in bash using 

cat info_qc.pass mac_qc.pass > extract_file.txt

and pass "extract_file.txt" to --extract in Regenie. This will be added to the enhancement features list.

Cheers, Joelle

joellembatchou commented 3 years ago

Multiple extract/exclude files are now allowed in v2.2.