Mutect2 - Bad input: GenomicsDBImport does not support GVCFs with MNPs
I'm running Mutect2 to generate PoN on four normal samples. It fails at the second step below.
a) GATK version used
b) Exact GATK commands used
gatk Mutect2 \
-R $ref \
-I $nBAM \
--max-mnp-distance 0 \
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
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.
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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