The Workflow of RNA-seq Data and Parameter for Snp Calling

[BrpTCP]

Dear developers,
I am a rookie in bioinformation and snp calling. There have some foolish questions when I doing my work.

• I don't know if I'm not careful, but I didn't see the detailed workflow for transcriptome snp calling in the GATK Best Practices Workflows. The workflow in some forums are not clear and meticulous. So I want to have a practise following the official workflow.
• Is there a parameter that requires only one read can identify a snp? This requirement will meet my needs.

All thanks to solve my problems!

[BrpTCP]

There is another questoin about the snp calling.
I have a credible dataset of snp of resequencing now. The variation data of my transcriptome needs to be compared with the snp of the resequencing data. If consistent, only one read can consider this SNP to be reliable. How to do that using GATK?