--exclude-if-info not mentioned in log file when no variants are filtered - expected behavior?

[Marta R.]

Hello!

I'm using PLINK2 to filter variants based on imputation quality (R2) and MAF. My input PLINK2 files from Michigan Imputation Server contain the R2 info field in the header:

##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy (R-square)">

I'm running the following commant:

plink2 --pfile input_data \
       --maf 0.001 \
       --exclude-if-info "R2 < 0.3" \
       --make-pgen \
       --out output_data

The command completes succesfully and the MAF filter is reported in the log file (attached down below) removing 88 million variants, but there is no mention of the --exclude-if-info "R2 < 0.3" filter in the log file. 

It's important to note that I know there's no variants that should be removed by this R2 < 0.3 filter as it was already filtered in TopMED imputation, but I still needed to confirm the filter again for an analysis. I also checked the amount of variants that were removed and all of them are from the MAF filtering. 

My questions are as followed:

1. Is it expected behaviour that --exclude-if-info is not mentioned in the log if zero variants are excluded by that filter? 

2. How can I confirm that PLINK2 actually evaluated the R2 field (even if no variants were removed)?

Thank you so much for any insight in advance!

Marta R. 

[Chris Chang]

1. Yes, that is the current behavior.

2. I will consider making this more obvious in the log in a future build, but in the meantime you could just see what happens when you increase the R2 cutoff.

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[Chris Chang]

Today's development build includes better logging for these variant filters.