Input data format from SnpSift

[a-qvecell]

Hello :)
Thank you for writing this!
I am keen to try it, and I attempt to follow the preprocessing steps described in your paper to prepare my mapped bam file for analysis.

I have annotated the SNPs using SnpEff and now I am to use SnpSift.
I haven't worked with this suite of tools before, so I was wondering if you could give me a hint as to how I should do the filtering:
What vcf entries are of interest for your program to get the necessary information and run properly?

I hope you can help.

Best,

Amanda :)