I'm trying to use ASEReadCounter to count reads per allele of some known indels, but got zero counts for altCount for all ~200,000 sites. But in haplotypecaller output vcf files, there're alternative allele reads. The ASEReadCounter output for SNPs (separate known snp site file) seem fine so far. Could you please let me know if ASEReadCounter can deal with indels?
Thank you very much!