Hi @weizhouUMICH ,
Regarding Step 1: I am using PLINK2, and I noticed that the current documentation (https://saigegit.github.io/SAIGE-doc/docs/set_step1.html) uses 2*$6-$5 to calculate allele thresholds. In PLINK2's default .acount output, column 6 ($6) is OBS_CT (the total number of observed alleles), which is already multiplied by 2 for diploids. Using 2*$6 multiplies this value a second time.
This has been discussed here: #34 (comment) but it was not updated in the documentation.
Is there a specific reason the documentation still doubles column 6 for PLINK2 files? Kindly let me know.
Thank you in advance!
Navya
Hi @weizhouUMICH ,
Regarding Step 1: I am using PLINK2, and I noticed that the current documentation (https://saigegit.github.io/SAIGE-doc/docs/set_step1.html) uses
2*$6-$5to calculate allele thresholds. In PLINK2's default .acount output, column 6 ($6) is OBS_CT (the total number of observed alleles), which is already multiplied by 2 for diploids. Using 2*$6 multiplies this value a second time.This has been discussed here: #34 (comment) but it was not updated in the documentation.
Is there a specific reason the documentation still doubles column 6 for PLINK2 files? Kindly let me know.
Thank you in advance!
Navya