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Alternate Alleles in VCF are more than 1 base

tc13tc13 Cambridge, UKMember

Hi there,

I've removed INDELS from a multi-sample vcf from HaplotypeCaller using SelectVariants. However, the ALT 'SNPs' are more than a single nucleotide substitution. Eg.


Q1) What is the meaning of the * symbol?
Q2) Is it to be expected that these SNPs are more than a single nucleotide substitution?


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Tom,

    1) Have a look at this dictionary entry.
    2) Sure, there can be INDELS that are much larger than one base. HaplotypeCaller can detect INDELs up to a read length, but if you are interested in larger INDELS, you should use a structural variant caller.


  • tc13tc13 Cambridge, UKMember

    Hi Sheila,

    I originally ran --selectTypeToExclude INDEL, though also including --selectTypeToExclude MIXED --selectTypeToExclude SYMBOLIC has resulted in a VCF with only SNPs.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Tom,

    I am glad that worked for you.
    Thanks for posting. This should help others in the future :smile:


  • CNBersCNBers Member

    @Sheila said:
    Hi again,

    Geraldine just let me know I misunderstood your question! I thought you were asking why INDELs are larger than one base. Sorry for the confusion.

    I suspect the SelectVariants tool in including the * allele as a "SNP" site. What was the exact command you ran?

    You can try using --selectTypeToExclude. I think if you add --selectTypeToExclude INDEL --selectTypeToExclude MIXED --selectTypeToExclude SYMBOLIC you will get only SNPs. Let us know if that is not the case.


    Dear Sheila,

    I want to remove the * allele and used --selectTypeToExclude INDEL --selectTypeToExclude MIXED --selectTypeToExclude

    But the * allele still in the output file.

    What should I do ? I use GATK3.8


  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi CNBers,

    1)The function to filter '* allele' has been fixed in the GATK version Upgrading to that should help resolve this issue.
    2) In cases where you want to drop sites with the * allele as the only ALT then, run SelectVariants with --exclude-non-variants

    Please refer to this documentation for more information: https://software.broadinstitute.org/gatk/documentation/tooldocs/

    Please let me know if this helps.

    Bhanu Gandham

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