I have rna-sequenced data from covid patients. I am using hisat2 for aligning the reads to reference. So, the resulted bam files after indexing are now ready. I would like to use gatk happlotypecaller for extracting variants from my bam files.
First, before calling haplotypecaller should I do any further analysis on my bam files?
Second, in the gatk forum HaplotypeCaller I see the sample commands but I noticed they are for DNA seq data. So, it means I cannot use gatk haplotypecaller for rna seq data? If yes, can you give me an example what would be the value for -ERC flag? if no, what else should I use?
Thanks in advance for any help.