We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Mutect2 not spitting the QUAL and GQ values

slpslp New YorkMember

Hello team GATK,
I am trying to implement Mutect2 on my matched TN paired bam files. Though I am getting calls in VCF format, The QUAL column is just "." and no values is given. Also the GQ values in the sample genotype columns is missing. I have used the below command:

java -Xmx8g -jar Tools/GATK_v3.5/GenomeAnalysisTK.jar -T MuTect2 -R Reference/Human/hg38/hg38.fa -I:tumor ALL_BAMS/"$TUMOR".sorted.dedup.realigned.recal.bam -I:normal ALL_BAMS/"$NORMAL".sorted.dedup.realigned.recal.bam
-stand_emit_conf 30 -stand_call_conf 30 --dbsnp Database/All_reorder.vcf
-L Database/Illumina_target/nexterarepdcapture_expandedexome_Intervals_hg38.bed -o ALL_BAMS/"$OUT"_TN.raw.vcf

Can you please suggest whats going wrong here?

Thanks
Sneh

Tagged:

Issue · Github
by Sheila

Issue Number
431
State
closed
Last Updated
Milestone
Array
Closed By
vdauwera

Answers

Sign In or Register to comment.