Differences in RNAseq Variant Calling and Allele Specific Expression
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4.8 years ago
serpalma.v ▴ 70

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 • 1.4k views
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