about Mutect2 usage
a) gatk-4.1.0.0 version
b) java 1.8
c) commands used
/usr/local/lib/gatk-4.1.0.0/gatk --java-options "-Xmx2g" Mutect2 \
-R /data/Reference/GRCh38/GRCh38.p12.genome.fa \
-I tumor.bam \
-I normal.bam \
-tumor tumor.bam \
-normal normal.bam \
-O 1_somatic_m2.vcf.gz \
-bamout 2_tumor_normal_m2.bam
d) Actually, after running Mutect2, I received "success" message
16:35:02.441 INFO Mutect2 - Shutting down engine
[March 4, 2020 4:35:02 PM KST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 20.71 minutes.
Runtime.totalMemory()=1856503808
Tool returned:
SUCCESS
However, vcf file does not contain varients like below
##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.
##normal_sample=10001625-TN.replaced.bam
##source=Mutect2
##tumor_sample=10001625-TT.replaced.bam
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10001625-TN.replaced.bam 10001625-TT.replaced.bam
========================================================
I tested another bam files, but none of the varients were detected
Any problem on my commands?
And, I changed the bam header like below to add read group(@RG)
java -jar picard.jar AddOrReplaceReadGroups \
I=normal.bam \
O=normal.bam \
ID=10001625-TN LB=10001625-TN-1 PL=illumina PU=10001625-TN SM=bam file full name
Regards
-
Sukjung Choi I'm confused because the Mutect2 command says that the normal sample name is normal.bam, but the output VCF header says it is 10001625-TN.replaced.bam. Could you double-check that the command line you posted is exactly the command you used to generate this output?
-
Thank you for your comment, David
my command is like that
/usr/local/lib/gatk-4.1.0.0/gatk --java-options "-Xmx2g" Mutect2 \
-R /data/Reference/GRCh38/GRCh38.p12.genome.fa \
-I 10001625-TT.replaced.bam \
-I 10001625-TN.replaced.bam \
-tumor 10001625-TT.replaced.bam \
-normal 10001625-TN.replaced.bam \
-O 1_somatic_m2.vcf.gz \
-bamout 2_tumor_normal_m2.bamSo, I add disable option
--disable-read-filter MappingQualityAvailableReadFilter \
Then, I could detect varients.
Is it all right?
-
If disabling the mapping quality available read filter is necessary to call variants, then something is wrong with your bam file. Because mapping artifacts are so common, it is very important for Mutect2 to have access to mapping qualities. What aligner are you using? Is there anything in your pipeline that might strip mapping qualities off of reads?
Please sign in to leave a comment.
3 comments