Paired-End Reads Alignment For Variant Calling ?

I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use BWA for mapping/alignment, followed by PiCard and GATK to do variant calling.

The question now is how to do sequencing alignment with BWA. Should I use the short paired end reads to generate a single SAM file, like this:

bwa mem -M -v 1 -t 4 human_genome_ref.fasta read_For.fastq.gz read_Rev.fastq.gz > read_PE.sam

is this okay? or should I map individual reads to reference separately?

thanks a lot for your reply.