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 🙂



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