Changes

''NOTE'': <code>--annoType Nonsynonymous</code> will only analyze nonsynonymous variants where they have <code>ANNO=Nonsynonymous</code> in the INFO field. VCF with annotatino information are called annotated VCF here. And to annotate a VCF file, you can use [https://github.com/zhanxw/anno ANNO], a fast and accurate annotation software.

''NOTE'': <code>--annoType Nonsynonymous</code> will only analyze nonsynonymous variants where they have <code>ANNO=Nonsynonymous</code> in the INFO field. VCF with annotatino information are called annotated VCF here. And to annotate a VCF file, you can use [https://github.com/zhanxw/anno ANNO], a fast and accurate annotation software.

== Genotyep filters ==

== Genotype filters ==

Genotype with low depth or low quality can be filtered out by these options:

Genotype with low depth or low quality can be filtered out by these options: