Differences in RNAseq Variant Calling and Allele Specific Expression

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6.2 years ago

serpalma.v ▴ 80

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!

RNA-Seq variant calling allele specific expression • 1.7k views

ADD COMMENT • link updated 13 months ago by afei • 0 • written 6.2 years ago by serpalma.v ▴ 80

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

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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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?

ADD REPLY • link 13 months ago by afei • 0

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