Question: Differences in RNAseq Variant Calling and Allele Specific Expression
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gravatar for serpalma.v
2.4 years ago by
serpalma.v40
Germany
serpalma.v40 wrote:

Dear community

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!

ADD COMMENTlink written 2.4 years ago by serpalma.v40

Ask on the GATK forum: https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum

ADD REPLYlink modified 18 months ago • written 18 months ago by Kevin Blighe61k
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