GATK GenomicsDBImport does not support GVCFs with MNPs

Question

[Rodolfo Adrián]

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 :)

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[Ram]

Rodolfo Adrián

Looks like you edited your post after I made the edit. Please see if you can format the post better. If not, I'll format it after a bit of time.

Answer 1

[Pierre Lindenbaum]

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

[Rodolfo Adrián]

Thank you for your help! :) I'll run Mutect2 with that option. I will update here the results.