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5.3 years ago
serpalma.v ▴ 70
Using the GATK's tools "haplotypecaller" and "ASEReadCounter" it is possible to produce a vcf file and a tabulated file for allele specific expression analysis (ASE), respectively.
The vcf file contains information about the number of reads mapping to each allele of a heterozygous position. I think this can be directly used for ASE.
If the vcf file contains allelic counts, why is there a tool specific for ASE?
Thank you in advance!
Ask on the GATK forum: https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you finally solved this problem?