uthrabalaji

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Username
uthrabalaji
Location
DALLAS
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Comments

  • Hi @Geraldine_VdAuwera , No, this bam is from a single run. Thanks, Uthra
  • Hi @Geraldine_VdAuwera , I tried to run MuTect with the -fixMisencodedQuals option and this is what I got. ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3…
  • Hi @Geraldine_VdAuwera , This is the mutect command I ran: /usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java -Xmx8g -jar /home/uthrabalaji/software/mutect-1.1.7.jar --analysis_type MuTect --reference_sequence /media/sf_F_DRIVE/Homo_sapiens/ReferenceF…
  • Hi @Geraldine_VdAuwera , I apologize for taking this long to respond. When I have 3 beds that I am using for my sequencing, would it still be good to use the intersection of all the 3? Is there any took that could find common intervals among 3 bed …
  • @Sheila and @Geraldine_VdAuwera : Thank you for the immediate respond. I really appreciate that. @Geraldine_VdAuwera : I downloaded muTect (1.1.7) and it seems to work fine for now. And I also noticed that it used GATK - 3.1 version. However muTect…