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KIR variant database downloaded?

arkilisarkilis BrisbaneMember
edited February 2015 in Ask the GATK team

Is the possible to have a target's kir variant database downloaded? I tried to download from some online sites, such as http://evs.gs.washington.edu/EVS, and barely find anything.

I followed your post here: http://gatkforums.broadinstitute.org/discussion/2604/input-files-known-and-reference-have-incompatible-contigs

Basically, I want to use the GATK generated all the variants of my sample, and want to filter specific target (KIR). Is that possible? Thanks!

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @arkilis
    Hi,

    I am not sure what exactly you are asking. You will have to ask KIR about downloading variants. However, once you have those variants, you can use SelectVariants to select all variants that overlap in GATK and KIR. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

    -Sheila

  • arkilisarkilis BrisbaneMember

    I just made a long explanation, but it seem lost once I click the "Post Comment" button.

  • arkilisarkilis BrisbaneMember

    Ok.

    I might need to use GATK to call variants of some particular regions of the samples. But according to your post, it was suggested to call all the variants first and then filter with part which you are interested. (using tool SelectVariants)

    But the question is when using SelectVariants, you have to provide the variants file (vcf) as it required in para -L.

    So my question is is there any way I can download this variants for these particular regions? Since everytime when I run it, it gives out a error msg said the contig does not math.

    2 INFO 14:45:45,860 GATKRunReport - Uploaded run statistics report to AWS S3
    13 ##### ERROR ------------------------------------------------------------------------------------------
    14 ##### ERROR A USER ERROR has occurred (version exported):
    15 ##### ERROR
    16 ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
    17 ##### ERROR The error message below tells you what is the problem.
    18 ##### ERROR
    19 ##### ERROR If the problem is an invalid argument, please check the online documentation guide
    20 ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    21 ##### ERROR
    22 ##### ERROR Visit our website and forum for extensive documentation and answers to
    23 ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    24 ##### ERROR
    25 ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    26 ##### ERROR
    27 ##### ERROR MESSAGE: File associated with name IntestedRegions.bed is malformed: Problem reading the interval file caused by Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 7113062 is less than start 7113063 in contig chr1

    Thanks in advance.

    Ben

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @arkilis
    Hi Ben,

    Can you post the exact command you used when you got this error message?

    Thanks,
    Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @arkilis You need to check that your BED file is formatted properly. It looks like some of the intervals have a stop position before the start position.

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