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?