Understanding filters used in plink

Question

[MAPK]

I am new to plink and genotype data and would like to ask about these filters below in plink. I ran this command below to get IBD values, but I am not very clear on --maf, --geno, --allow-no-sex and --ld-window-r2 filters. I looked at the explanation on Plink's website, but I am not sure if I understood it completely. Can someone please help me understand these filters in simple terms. Thanks for your help in advance

plink1.9 --bfile bfile --genome --min 0.06 --maf 0.2 --geno 0.01 \
    --hwe 10e-6 --allow-no-sex --ld-window-r2 0.2 --out outfile

[zx8754]

Plink is very well documented, what is not clear about these flags' definitions?

[Kevin Blighe]

Indeed, MAPK, PLINK's documentation is pretty good. In order to avoid somebody feeling that they have to elaborate on each parameter that you have listed, it would be much better if you explained very specifically where your doubt lies.