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

Ask on the GATK forum:

ADD REPLYlink modified 22 months ago • written 22 months ago by Kevin Blighe66k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 819 users visited in the last hour