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HaplotyperCaller optional arguments:

Hello GATK,

I'm using GATK 4.0.6 HaplotypeCaller to call wild bird SNP and InDel sites.

nohup java -jar /opt/GATK-4.0.6/GATK-4.0.6-local.jar HaplotypeCaller -R bird_genome_reference.fa -I input.bam --minimum-mapping-quality 25 -mbq 13 -O VCF_two_type/HC.vcf --output-mode EMIT_VARIANTS_ONLY &

When I check the output in nohup, I notice that there are many optional arguments in the nohup file.
But I didn't see some of them in the ToolDoc of HaplotypeCaller.

Why do not put all the available arguments in the ToolDoc?

I want to set the threshold condition of two short variants caller(bcftools mpileup & HaplotypeCaller) the same as possible and then get the consistent short variants site with SelectVariants to improve my SNP & Indels quality.


Best Answers


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    Accepted Answer

    Hi @tytolin

    What are all the arguments you see that are not in the tooldoc?


  • tytolintytolin Member
    Accepted Answer


    I have seen it in the Read Filter, thanks.
    Sorry for neglecting other parts of category

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    no problem. happy to help.

  • maricommaricom Member
    I'm using HaplotypeCaller to find variants, however, could you tell me about the --minimum-mapping-quality option?
    If I set this option, what kind of calculation does GATK do??
    I read this page, but I need more detailed information.

    Thank you in advance!
  • maricommaricom Member
    Sorry I couldn't paste the link for the page.
    In the page, there is an explanation of the meaning of the option, but I can't tell what kind of reads will be eliminated after I apply this option.
  • bshifawbshifaw Member, Broadie, Moderator admin

    This argument is valid if "MappingQualityReadFilter" is specified which Haplotypecaller automatically does:

                                      Maximum mapping quality to keep (inclusive)  Default value: null. 
                                      Minimum mapping quality to keep (inclusive)  Default value: 20. 

    Tool doc for MappingQualityReadFilter says:

    Keep only reads with mapping qualities within a specified range.
    Note: this filter is not designed to handle the unavailable mapping quality (255). Use MappingQualityAvailableReadFilter to explicitly filter out reads with unavailable quality.

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