no read counts per allele while using gatk ASEReadCounter
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2.0 years ago
Sara ▴ 260

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?

GATK • 396 views

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