What filtering steps are required for the VCF file input to gimbleprep?

[kuangzhuoran]

I generated a VCF file using FreeBayes, and I noticed that gimbleprep includes some options for SNP filtering.

Besides those, should I also filter out missing data, low minor allele frequency variants, and indels before running gimbleprep?

[GertjanBisschop]

Converting to discussion. This might be useful to others.