Hi,

I have a RNA-seq .BAM file for each patient. Also, for each patient I have done whole genome sequencing and I have .BAM files. By strelka I called mutations and I got .vcf. Now, when I used .BAM file of RNA-seq and .vcf file from WGS for allele specific expression analysis by gatk, I got an empty file

This is the command I used

gatk ASEReadCounter \
    -R hs37d5.fa \
    -I RNA-seq.bam \
    -V WGS.vcf.gz \
    -O output.table

Can any of you done allele specific expression analysis help me to see where I am doing wrong? Should I first call mutation on RNA-seq .BAM files and use that instead of WGS?

Any comments?