VariantAnnotator QualByDepth - no error and no annotation..
Hi, I am new to exome-seq and would be grateful for any help :) I want to use VariantAnnotator to annotate variants with QualByDepth, variants were called with MuTect2.
I do not get any error, however there is no QD field in my output vcf..
I use GATK 4.1.8.1 version. Here is my code:
gatk VariantAnnotator \
-V MuTect_output.vcf \
-R Homo_sapiens.GRCh38.dna.toplevel.fa \
-I finalbam-output.bam \
-A QualByDepth \
-O VariantAnnotator_QD.vcf
Is QualByDepth annotation specific to HaplotypeCaller?
I would be most grateful for any suggestions!
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Hello wiki97, here is a troubleshooting document: https://gatk.broadinstitute.org/hc/en-us/articles/360035532272-Missing-annotations-in-the-output-callset-VCF
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Dear Genevieve Brandt, thank you very much for your answer!
I have already read this article, however I am not sure what is the reason for the lack of this specific annotation..
Is QualByDepth specific to HaplotypeCaller? Or is it already applied by default in MuTect2 output but in a different name? I provided BAM file, so it is not the case of "optional input".
I would be most grateful for any suggestions :)
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Hi wiki97, I believe it should be available in Mutect2 as well. Here is the documentation for the QualByDepth annotation. Are QUAL and AD present in your VCF?
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Dear Genevieve Brandt, thank you very much for your answer.
Yes, I do have AD values but I have just realized what the problem is - in the QUAL column I cannot find any values, there are dots in all rows.. Does it mean that I didn't run Mutect2 correctly?
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wiki97 were there any errors or warnings in your Mutect2 run?
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No, there were no warnings/errors.. I received the "SUCCESS" message from MuTect2.
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wiki97 could you post a few example variants here?
Please also run ValidateVariants to confirm that there are no issues with the file. You can follow this tutorial to check for error messages and what they mean.
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I run ValidateSamFile and got "No errors found" message, the ValidateVariants gave "Processed 89324 total variants in 8.6 minutes" message and no error/warning information.
Here are first few lines of my MuTect2 output:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT lane
1 13417 . C CGAGA . . AS_SB_TABLE=1,0|5,5;DP=16;ECNT=1;MBQ=34,31;MFRL=255,263;MMQ=22,23;MPOS=21;POPAF=5.60;RPA=2,4;RU=GA;STR;TLOD=41.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,10:0.855:11:1,5:0,3:1,0,5,5
1 14599 . T A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,27;MFRL=0,246;MMQ=60,22;MPOS=10;POPAF=0.831;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:14599_T_A:14599:0,0,1,0
1 14604 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=31,36;MFRL=291,246;MMQ=23,22;MPOS=5;POPAF=0.831;TLOD=3.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:1,1:0.500:2:0,0:1,1:0|1:14599_T_A:14599:1,0,1,0
1 629906 . C T . . AS_SB_TABLE=0,0|3,0;DP=5;ECNT=1;MBQ=0,34;MFRL=0,159;MMQ=60,27;MPOS=41;POPAF=0.228;TLOD=8.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,3:0.810:3:0,2:0,1:0,0,3,0 -
Mutect2 does not emit the QUAL column. The `_____Q` annotations are essentially qual scores for individual filters. You can read more about the Mutect2 filters in the ToolDocs page or in the algorithm paper.
The recommended method for variant filtering with Mutect2 results is FilterMutectCalls, which takes into consideration the differences that will occur in a somatic VCF. Here is more information.
There is an archived post regarding this issue on our old forum website, archived at this site.
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Ok, thank you very much for your help!!
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