I have mentioned something to your earlier query in the variant calling thread. Take a look. Since you are doing it for the first time. It is always advisable to run each steps manually and do a thorough check of each of them with the plots so that you can get a hang of what exactly GATK is doing. It is a great resource but can be cumbersome owing to its thorough modules and too much of documentation. So it is advisable to check it carefully. As far filtering the vcf file, I would kindly ask you to look here as I mentioned under your comment.

Once you are aware of the entire workflow you can always make an automate workflow for future purposes. Good Luck!