I am using gatk ASEReadCounter to get the read counts per allele. To do so, I used the following command:
gatk ASEReadCounter -R /path_to_genome/hg38_genome/GRCh38.p13.genome.fa -I sample.sorted.bam -V sample.vcf.gz -O output.table
I am not getting any error but output.table file has only header. All the input files in the above command have index file too. I checked the vcf file and bam file and both have similar chromosome notation (with chr in the beginning of chromosome names). vcf file has only SNPs and heterozygote ones. I used GATK4.
Do you know what the problem could be?