Mutect2 - Bad input: GenomicsDBImport does not support GVCFs with MNPs

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Anish Bhaswanth

• March 09, 2020 14:48

I'm running Mutect2 to generate PoN on four normal samples. It fails at the second step below.

a) GATK version used

gatk v4.1.5.0

b) Exact GATK commands used

gatk Mutect2 \
        -R $ref \
        -I $nBAM \
        --max-mnp-distance 0 \
        -O $out/${sample}.pon.vcf.gz

gatk GenomicsDBImport -R $ref -L $interval_list \
     --genomicsdb-workspace-path $out/pon_db \
     -V $out/BM1.pon.vcf.gz \
     -V $out/BM2.pon.vcf.gz \
     -V $out/BM3.pon.vcf.gz \
     -V $out/BM4.pon.vcf.gz \

c) The entire error log if applicable.

A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at chr1:1266056 in VCF

~/Variant_Calling/Mutect2/PoN/BM01.pon.vcf.gz

Below is the position in the VCF file.

chr1    1266056 .   AACCA   TGGTT   .   .   DP=16;ECNT=3;MBQ=31,20;MFRL=228,139;MMQ=60,60;MPOS=8;POPAF=7.30;TLOD=6.87   GT:AD:AF:DP:F1R2:F2R1:SB    0/1:12,2:0.152:14:1,0:9,2:8,4,1,1

 

Is there a workaround this? I read through other discussions but could not find anything helpful.

 

Thanks!

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• 

  Bhanu Gandham

  • March 10, 2020 19:24

  Hi Anish Bhaswanth

   

  This is a known issue and we looking into this. However, it will help us fix this faster if you could share your input BAM file. You can find instructions for sharing BAM here: https://gatk.zendesk.com/hc/en-us/articles/360035889671

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