Filtering in TASSEL- regarding

[Vijay Rajamanickam]

Dear Folks,

Is it fine to set the following criteria (in the image) for filtering and quality control of genotypic data.?

What does it mean?

Site Max allele freq: 0.5

max heterozygous proportion: 0.2

is this QC enough for GWAS analysis?

-----------kind regards------------

Vijay R,

PhD Scholar (Plant Physiology),

IARI, PUSA Campus

New Delhi-110012