Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.

AsJ

About

Username
AsJ
Location
JP
Joined
Visits
50
Last Active
Roles
Member
Points
12
Badges
3
Location
JP

Comments

  • Hi VdAuwera, Yes, I am running this with both tumor and normal bams.
  • Hi, Thank you for the answer. I have tried running CountReads and i got the same number of reads as samtools or wc -l file.sam. This means that the log message by Mutect2 was not correct. ------ java -jar GenomeAnalysisTK.jar -R reference.fa -T…
  • Thnks for the reply. I think there is something strange in counting the number of reads. I counted the reads using wc -l file.sam and samtools flagstat I got same number of reads using both wc -l file.sam and samtools flagstat ==== samtools flags…
  • Thank you !
  • Thank you for the answer. Would you please explain more how muTect2 use the proper sample names and why tumor and normal sample names are not sufficient?
  • Thank you very much. So How can i use t_ins_count and t_del_count in result interpretation??