Allele-specific expression from bulk tumor RNAseq

Question

[mjs2225]

Hi,

I am trying to get allele-specific expression from bulk RNAseq for somatic variants called from whole-exome DNAseq. Mainly, I would like to check if somatic variants in DNA are also being expressed in RNA. I have tried tools like Isovar and RNA-mutect (thought I understand that RNA-mutect is more for denovo variant calling). I am seeing poor concordance in rna alt read counts between these two tools. I have the following questions:

• Any suggestions from the community on what would be a good/latest tool to use extract rna alt read counts?
• Is it recommended to remove duplicate reads from RNAseq before calculating the alt read counts? This seems like a long standing debate but seems like RNA-mutect is doing deduplication which dramatically changes the alt read counts pre- an post- dup filtering.

Thanks,
Minita