Genotyping precalled sites/variants

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Reto Burri

• May 29, 2020 08:18
• Edited

I am looking for a way to genotype a specific set of variants/sites in GATK4.1.4.1. In previous versions it was possible to provide a sites-only vcf (back then to UnifiedGenotyper) to have all these sites genotyped. However, I cannot find this option in genotypeGVCFs.

Background: I have populations/species with highly stratified allele frequencies, and I want to genotype these separately to not bias the genotypes by the allele frequencies in the entire set of individuals. To still get the same sites called, however, I have to provide a list of sites/variants.

Thanks a lot for any insights!
Reto

 

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  Bhanu Gandham

  • May 29, 2020 17:02

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

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  ABours

  • May 29, 2020 18:52
  • Edited

  Hi Reto,

  You can actually provide a list to GenotypeGVCFs to opporate on, it's the -L function. You can specify in that list single sites. I haven't tried it, but otherwise you could take a region of 100 bp before and after the variant you definitely want to call.

  for example you can format it as such, and save it as a list:

  for a site:
  chr_5:100
  chr_6:15890
  chr_7:4389
  
  for a region:
  chr_5:50-250
  chr_6:25790-15990

  I haven't tried this myself, but I think it should work. Also if the site isn't a variant in your new vcf it will not appear (unless you say --include-non-variant-sites this will ensure that you have all callable site)

  I hope this can help you :)

  Cheers,

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  Bhanu Gandham

  • June 01, 2020 13:55

  ABours you are right -L can be used to restrict tool to certain sites. You can even provide vcf as input to -L.

   

  Thank you so much ABours for pitching in and helping out the GATK community! We appreciate your help with building the GATK Knowledge-base!

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