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Call variant from RNA-Seq data using Haplotypecaller

Hi
My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq data. However, RNA-Seq has different (more complicated) allele frequency. How comes that Haplotypecaller is still being used in RNA-Seq variant calling pipeline? Can anyone share some information on this question? Really appreciated

Issue · Github
by Sheila

Issue Number
1398
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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