Genotype calls for a list of variable sites

Question

[Jautis]

Hi,

I have a list of variable sites identified in a previous study of the same population. I would like to call genotypes in a set of new samples specifically at those sites. How can I do so?

I think this is a mix between -L commands to select a particular chromosome region and using a dbSNP file to give prior information about known variants. The difference is that I am only interested in testing the known variants, not in identifying new ones, and I don't care whether the site would pass filtering in the new dataset, only that the genotype call for an individual is reliable assuming the site is known to be variable.

Thank you very much!

Answer 1

[Pierre Lindenbaum]

• call with GATK + option -L vcf_to_bed.bed (or -L ref.vcf should work too )
• use SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php with option --concordance

[Jautis]

That's useful, but is there a way to always call the sites, even if there isn't enough information to identify a variable site in the new dataset?