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Dear GATK team,
I am doing an allele-specific expression analysis using RNA-seq data. I am trying to run ASEReadCounter to calculate read counts per allele and use Mamba (or other downstream tool) for the allele-specific expression analysis.
My question is: which bam file I should have as an input for the ASEReadCounter do you recommend. Is the bamout file generated by HaplotypeCaller that was after local assembly and re-alignment better? or should I just input the pre-processed and aligned RNA-seq?
Thank you in advance for your help.