what it means the NO CALL from GATK

ibseqibseq United KingdomMember

Hi all,
just curious to know what exactly means that for certain SNPs we read ""NO CALL" on our vcf file, despite not been filtered out?

thanks
irene

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited May 2018

    @ibseq
    Hi Irene,

    ./. or no-call genotypes occur when the tool does not have enough information to make a proper genotype call. This could be due to low coverage or bad quality data or messy regions in general.

    -Sheila

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