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?

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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).

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