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tianshilu / QBRC-Somatic-Pipeline

QBRC Somatic Mutation Calling Pipeline
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Problem with GATK3 #16

Open ysq1770368148 opened 2 years ago

ysq1770368148 commented 2 years ago

Hi @tianshilu, You uesd GATK3 in the somatic.pl,but now when I use GATK3, the RealignerTargetCreator, IndelRealigner and PrintReads function of GATK3 can not be found in my GATK3,may be GATK4 replaces GATK3. But when I use GATK4, it has errors with RealignerTargetCreator, IndelRealigner and PrintReads function.Someone said that RealignerTargetCreator and IndelRealigner had little impact, so I wonder if this is ok to use GATK4 in your somatic.pl without RealignerTargetCreator and IndelRealigner steps.

A USER ERROR has occurred: IndelRealigner is no longer included in GATK as of version 4.0.0.0. Please use GATK3 to run this tool

Thanks!

wtwt5237 commented 2 years ago

Hi, @ysq1770368148

This is a little weird, as I thought we included GATK3 in our /somatic_script folder, and our pipeline uses this GATK3. Did you modify our codes to use your own GATK3?

We haven't tested whether our pipeline works with GATK4 yet

Thanks!

Tao