Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

What means is " * " in alternative allele ?

SunhyeSunhye KoreaMember
edited October 2015 in Ask the GATK team

Hi.
I ran HaplotypeCaller about multi-samples to obtain gvcf and combined multi-samples's gvcf using GenotypeGVCF.
As result of GenotypeGVCF, I obtain joint,vcf.
However, I couldn't understand contents in my joint.vcf,

10      134767  rs12768206      A       G,*     11674.12        .       AC=30,4;AF=0.246,0.033;AN=122;BaseQRankSum=-1.260e+00;ClippingRankSum=0.458;DB;DP=1662;FS=1.110;InbreedingCoe

What means is " * " in alternative allele column and What is genotype?

Best Answers

Answers

  • SunhyeSunhye KoreaMember

    thanks! Sheila!

  • SunhyeSunhye KoreaMember
    edited October 2015

    In that case, " G,* " in ALT column is multi-alleleic SNVs? or both SNP and Indel ?
    Why were only upstream deletions assigned specific character?

  • SunhyeSunhye KoreaMember

    Thanks ! @Sheila and @SteveL !
    Thanks to you, I have solved this question.
    In this case, I have been considering continually how to analyze or process(ex. what to filter or remain these sites).

Sign In or Register to comment.