Hi, I'm new to using GATK and I am currently facing the same issue when I want to run GenomicsDBImport following the pipeline that GATK. I ran Mutect2 in tumor only mode my set of normal BAMS, there were no errors according to the log files. Next, I ran GenomicsDBImport but I keep getting the following:
A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at 1:134834378 in VCF /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6753c_PON.vcf
I'm currently working with gatk v.4.1.5.0
The commands I run for Mutect2 tumor only mode are the following:
gatk Mutect2 -R /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GRCm38_68.fa \
-I /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/MOUSE_GRCm38_pulldown_MD6753c.dupmarked.bam \
--max-mnp-distance 0 \
-O MD6753c_PON.vcf
(I ran the same structure for other 4 normal samples)
The GenomicsDBImport command:
gatk GenomicsDBImport -R /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/GRCm38_68.fa \
-L /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/Mouse_GRCm38_Exome_Targets_67.bed \
--genomicsdb-workspace-path pon_db \
-V /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6753c_PON.vcf \
-V /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6754c_PON.vcf \
-V /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6755c_PON.vcf \
-V /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6756c_PON.vcf \
-V /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6758c_PON.vcf
The entire error log:
A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at 1:134834378 in VCF /mnt/Adenina/drobles/rarriaga/outputVC/Variant_Calling/GenomicsDBImport/MD6753c_PON.vcf
Is there any way to get around this issue?
Thanks in advance, I appreciate your help :)
As far as I see you're NOT generating GVCF file. You should use --emit-ref-confidence GVCF https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2#--emit-ref-confidence . Furthermore, you'd better name your files with the '.g.vcf.gz' suffix
Thank you for your help! :) I'll run Mutect2 with that option. I will update here the results.
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