I am trying to identify variants of tumour paired-end RNA-seq data using Mutect2. Please ignore more advanced operations such as using tumour and normal matched sample pair or PoN creation. I will use a simple example here.

I used MACS2 to map a pair of fastq files of R1 and R2 on the genome (I used CDS sequences as 'genome', thus MACS2 might able to be used for RNA-seq) and generated a bam file containing paired-end reads. As you can see in the image below it has many variants relative to the genome (e.g. BAM image in IGV: changed from G to A at position 156).
But when I try to use mutant2 to identify variants such as position 156 (covering the entire genome)：

java -Xmx1t -jar gatk-package-4.2.6.1-local.jar Mutect2 -R current.genome.fa -I cancer_T1.sorted.bam --native-pair-hmm-threads 50 --max-mnp-distance 0 -O test_cancer_N1.sorted.vcf.gz --bam-output test.bam

The output is 0 variant found:

$ zcat test_cancer_N1.sorted.vcf.gz | head

    ##fileformat=VCFv4.2
    ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
    ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
    ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
    ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
    ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
    ##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele.">
    ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">

$ zcat test_cancer_N1.sorted.vcf.gz | tail

    ##contig=<ID=CCDS87784.1|Hs109|chrX,length=2697>
    ##contig=<ID=CCDS87786.1|Hs109|chrX,length=1002>
    ##contig=<ID=CCDS87789.1|Hs109|chrX,length=471>
    ##contig=<ID=CCDS87792.1|Hs109|chrX,length=1737>
    ##contig=<ID=CCDS87793.1|Hs109|chrX,length=1110>
    ##contig=<ID=CCDS87800.1|Hs109|chrX,length=714>
    ##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
    ##source=Mutect2
    ##tumor_sample=cancer_N1
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  cancer_N1

All other paired-end RNA-seq data, regardless of species, produced almost no variant results like the above example. When splitting R1 and R2 into single-end and calling variants separately, a large number of variant results will be produced for each of them. 
I don't understand what I'm doing wrong with paired-end RNA-seq data, or that Mutect2 was not originally designed for paired-end RNA-seq data. 

I know it is wrong to split paired-end into two single-ends and run them separately, it will miss a lot of information. Ask for any valid suggestions to get paired-end RNA-seq data working properly in Mutect2.