HaplotypeCaller and reads mapped to multiple locations

Dear GATK team,

I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted, but it seemed hard to find out about this information, so I hoped to get some advice or pointed to the right place - How does the HaplotypeCaller handle reads mapped to multiple places? I used paired-end reads for read mapping.

Thank you very much for any feedback you might have.

Sincerely,

Xin