The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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!