PON: Mutect2 include MNPs and crash GenomicsDBImport

manolismanolis Member ✭✭
edited April 20 in Ask the GATK team

GATK v4.1.1.0, linux server, bash


using the following command I create the input files for the pon:

${gatk}  Mutect2 \
-R ${hg38} \
-I ${bqsr_bam} \
-O ${sample_pon} \
-L ${intervals}

When I run GenomicsDBImport I have an error which reports the presence of MNPs in the ${sample_pon} files

Then I exclude the MNPs with:

${gatk} SelectVariants \
-R ${hg38} \
-V ${sample_pon} \
-O ${clean_sample_pon} \
-xl-select-type MNP

If I go to count the variants before and after SelectVariants I have the following counts



How can I deactivate the call of MNPs in Mutect2 in order to use GenomicsDBImport?
Is it the default behavior of Mutect2/pon-pipeline or I'm doing something wrong?

Many thanks

Post edited by manolis on

Best Answer


  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Neither GenomicsDBImport does support mutect2 nor does mutect2 have a gvcf mode. How can you import them in the first place?

  • manolismanolis Member ✭✭

    Hi @SkyWarrior !

    In the last version, v4.1.1.0, according to the pon pipeline you can use M2+GDBI+CreateSomaticPanelOfNormals in case you have to process a large number of samples, this is what I understand, hoping correctly...

           gatk GenomicsDBImport --genomicsdb-workspace-path pon_db -R ${ref_fasta} -V ${sep=' -V ' input_vcfs} -L ${intervals}
            gatk --java-options "-Xmx${command_mem}g"  CreateSomaticPanelOfNormals -R ${ref_fasta} --germline-resource ${gnomad} \
                -V gendb://pon_db -O ${output_vcf_name}.vcf ${create_pon_extra_args}

    I found my error, in HC the default value of "--max-mnp-distance" is 0 but in the M2 tool is 1.

    I ran M2 with the value 0 and then I filtered the MNPs with SelecteVariants... now, before and after SelectVariants the number of variants is the same... just for a fast check.

    @bhanuGandham, please, is correct the solution of my post?


  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited April 21

    Wow this is uncalled for. Changing a default parameter is really dangerous. I guess this must be reverted in the next version.

    Also another user is reporting a similar problem with haplotypecaller and combinegvcfs. Is it possible the MNPs are somehow emitted due to some parameter change and nobody is really aware of. I have to check my own GVCFs. I have not done joint genotyping for a long time.

  • manolismanolis Member ✭✭
    edited April 21

    Personally I ran the CNN pipeline and now I want to run the GDBI-VQSR pipeline because I want to compare the outputs.

    Moreover, if I'm going to create a pon file with Mutect2 "--max-mnp-distance 0", then when I'm going to use this pon with a tumor sample (somatic SNPs/Indels discovery) again in the Mutect2 I have to set up 0, correct?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    That sounds the most logical way.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @SkyWarrior and @manolis,

    I agree that is weird. Let me check with the dev team and get back to you shortly.

  • syer89syer89 Member
    Hi @bhanuGandham , I have same problem with v4.1.2.0 GenomicsDBImport for creating PON and I wanted to confirm this bug is still active in the new version as well, and we continue using --max-mnp-distance 0 with Mutect2 ?
  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    It appears that this issue has not been closed. You can follow the progress on github here

  • syer89syer89 Member
    edited May 20
    Hi @AdelaideR @davidben . That seems like a different issue (unless I got it wrong). When creating PON it's advised to use Mutect2 "--max-mnp-distance 0" as GenomicsDBImport cannot handle otherwise. When compared the results between default (1) and 0 and results look like expected and not like in the issue above.
    When now analyzing a tumor sample with Mutect2 with this PON downstream, is it tested that it works with default --max-mnp-distance or should we use the same "--max-mnp-distance 0" for sample processing as well ? Please advise.
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