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GQX values in gvcf

I found this description of the GQX value that is potentially available in a gvcf on the illumina website.
The description implies this could be used to filter fairly/equally the variant and nonvariant sites.
I don't see this available with GATK, and I wondered if this was going to be something that could be added in the future.

Best Answers

Answers

  • prepagamprepagam Member

    Hi Geraldine
    Thanks, that make sense. I guess the GQX value sounded different because they imply you can filter variant and non-variant sites fairly with it, whereas you can't use GQ and RGQ in that way e.g. filter both with a value of 20 to get similar stringency of filtering variant and nonvariant sites (or perhaps I misunderstood illumina's description). It seems that filtering of nonvariant sites is a somewhat under studied area.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @prepagam
    Hi,

    For filtering non-variant sites, you can look at the QUAL score, rather than the GQ score. Have a look at this article.

    -Sheila

  • prepagamprepagam Member

    Hi Shelia
    I guess the concern is how to filter with similar stringency for variant and non-variant sites. QUAL will always be lower for non-reference, so if i filter via QUAL, then I will overly filter the variant calls.

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