GATK workflow for de novo transcriptome assembly of non-model organism

Question

[poecile.pal]

Good morning,

Using hisat2, I mapped reads on transcripts_longestiso_longorfs.fasta (de novo transcriptome assembly of non-model organism) and obtained .sam file. Using samtools, I converted it to .bam, sorted and indexed:

samtools view -bS hisat2_map_learn.sam > hisat2_map_learn.bam 
samtools sort hisat2_map_learn.bam hisat2_map_learn_sorted
samtools index hisat2_map_learn_sorted.bam

Please tell me where can I find the verified workflow of using GATK to search for SNP in my case?

Best regards, Poecile