Question: Dear Biostars,

This question specifically is about the best practice of using GATK4 to look for snps and indels in human samples.

I am fairly new to genomics and I think I am misunderstanding how GATK have separated their `--known-sites` during BSQR and VSQR steps.

During BSQR (`BaseRecalibrator`) I believe the generic `--known-sites` used for human analysis are: dbsnps, Homo_sapiens_assembly38.known_indels, and Mills_and_1000G_gold_standard.indels. Also on a few posts online I saw the use of 1000G_phase1.snps.high_confidence.hg38 and 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.

However when is comes to VSQR (`VariantRecalibrator`) the `--resource` flag changes some of these up. For example, in the standard example given on the Broad website (https://gatk.broadinstitute.org/hc/en-us/articles/360036351392-VariantRecalibrator), 1000G_phase1.snps.high_confidence.hg38 is now `known=false`, and dbsnps is the only dataset given the `known=true` flag.

I am confused to why BSQR and VSRQ steps can alternate which resources are classed as known. Is there a reference online to state which of the GATK resource bundle datasets should be used as known?

The GATK forum had a similar question, but I did not find the query to be answered decisively. (https://gatk.broadinstitute.org/hc/en-us/articles/360035890831-Known-variants-Training-resources-Truth-sets).

Any insight from more experience bioinformaticians on which datasets are most appropriate as `known-sites` would be a big help.

Cheers

Answer: First of all, thank you for a very clear Q and also for all the efforts you have made for nice formatting.

If you read the description of `known` on the VQSR page (https://gatk.broadinstitute.org/hc/en-us/articles/360036351392-VariantRecalibrator)

> **--resource / -resource**
> Known - The program only uses known sites for reporting purposes (to indicate whether variants are already known or novel)

So, known sites are used only to *nominate* if a site has already been reported to be found elsewhere (known or novel). In this respect, it is imperative to take `dbsnp` as the most qualified resource, as they collate snp information from all other sources. See these

https://www.internationalgenome.org/faq/are-the-igsr-variants-available-in-dbsnp/

https://www.biostars.org/p/18299/

Other SNP resources could be used for 'truth' and 'training' sets, which is explained in the 2nd link that you posted

> A **training set** resource is a list of variants that is used by
> machine-learning based algorithms to model the properties of true
> variation vs. artifacts. This requires a higher standard of curation
> and validation of the variants that are included in the resource.
> Tools that take such a resource typically accept a parameter that
> indicates your degree of confidence in the resource. This type of
> resource is difficult to bootstrap, as it benefits greatly from
> orthogonal validation (e.g. through a different technology such as
> arrays or Sanger sequencing).
>
> A **truth set** resource is a list of variants that is used to evaluate
> the quality of a variant callset (e.g. sensitivity and specificity, or
> recall). As such this requires the highest standard of validation, and
> tools that take such a resource will assume all variant calls it
> contains are true variation. This cannot be bootstrapped and must be
> generated using orthogonal validation methods.

As you see, the training set requires a higher degree of confidence and the truth set requires the highest degree of confidence - so you can choose them according to your confidence level.

For example, calibrating exome SNP data, different resources have been used for training and test sets. (see the link above)

>
> **--resource:hapmap,known=false,training=true,truth=true**,prior=15.0 hapmap_3.3.hg38.sites.vcf.gz \
> **--resource:omni,known=false,training=true,truth=false**,prior=12.0 1000G_omni2.5.hg38.sites.vcf.gz \
> **--resource:1000G,known=false,training=true,truth=false**,prior=10.0 1000G_phase1.snps.high_confidence.hg38.vcf.gz \
> -**-resource:dbsnp,known=true,training=false,truth=false**,prior=2.0 Homo_sapiens_assembly38.dbsnp138.vcf.gz \

Using `dbsnp' has another advantage that it collects SNPs from other species. So you have single 'known' database for SNPs in all species.

**BQSR**

The `--known-sites` argument is used a little bit differently in BQSR
(https://gatk.broadinstitute.org/hc/en-us/articles/360036898312-BaseRecalibrator#--known-sites)

> **--known-sites / NA**
> One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. **This
> algorithm treats every reference mismatch as an indication of error.
> However, real genetic variation is expected to mismatch the reference,
> so it is critical that a database of known polymorphic sites is given
> to the tool in order to skip over those sites.** This tool accepts any
> number of Feature-containing files (VCF, BCF, BED, etc.) for use as
> this database. For users wishing to exclude an interval list of known
> variation simply use -XL my.interval.list to skip over processing
> those sites. Please note however that the statistics reported by the
> tool will not accurately be reflected those sites skipped by the -XL
> argument.

So here you would give any/all sites, which has *potential* to be a SNP