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Working with SNPs

Source: vignettes/variants.Rmd
variants.Rmd

This vignette describe how to use the variant endpoints which store information about SNPs used in the smarter genotype datasets.

Assembly versions

One of the aim of this project is to manage genotypes in different assembly version. This means collect data from different assemblies (due to when data is generated), from different sources (Affymetrix, Illumina, WGS) and different file formats. Genotypes are normalized in order to be consistent accross data sources and stored in one genotype file for each specie.

Currently four assembly versions are managed, two for the sheep dataset and two for the goat dataset. Information about assemblies data sources can be retrieved from the backend info endpoint through the get_smarter_info() function:

info <- get_smarter_info()
assemblies <- as.data.frame(t(as.data.frame(info$working_assemblies)))
names(assemblies) <- c("name", "source")
  name source
ARS1 ARS1 manifest
CHI1 CHI1.0 SNPchiMp v.3
OAR3 Oar_v3.1 SNPchiMp v.3
OAR4 Oar_v4.0 SNPchiMp v.3

Collect data from an assembly

get_smarter_variants() have two mandatory parameters, species and assembly, then it could accept additional parameters (see one of the variant endpoints to have more information). For example you can search variants for snp name or rs id (if the latter exists):

snp <- get_smarter_variants(
  species = "Goat",
  assembly = "ARS1",
  query = list(
    name = "snp12965-scaffold1499-3295573"
  )
)
Table continues below
affy_snp_id chrom date illumina illumina_strand
Affx-122936132 8 2021-01-08 T/C BOT
Table continues below
illumina_top imported_from position strand version
A/G manifest 66621364 BOT ARS1
name probesets rs_id
snp12965-scaffold1499-3295573 AffymetrixAxiomGoatv2 rs119103301

Please, refer to the get_smarter_info() working_assemblies to have an idea of the assemblies supported by the SMARTER-database. Data which come from SNPchiMp v.3 like the Sheep OAR3 assembly, support the illumina forward attribute. For example the following SNP:

snp <- get_smarter_variants(
  species = "Sheep",
  assembly = "OAR3",
  query = list(
    rs_id = "rs10721092"
  )
)
Table continues below
chip_name alleles chrom illumina illumina_forward
IlluminaOvineHDSNP C/T 18 T/C T/C
Table continues below
illumina_strand illumina_top imported_from position ss_id
bottom A/G SNPchiMp v.3 64249211 ss896246690
strand version name rs_id
forward Oar_v3.1 oar3_OAR18_64249211 rs10721092

Is T/C on the forward strand of OAR3: this means that the reversed probe is aligned to the genome (as you could infer from the bottom illumina strand attribute of this SNP). Genotypes in the SMARTER-database are converted using the illumina top coding convention, so you will find this SNP as A/G in the SMARTER-database while on the reference sequence it’s T/C.

Fetch Variants by region

Variants endpoint support query by regions, using <chromosome>:<start>-<end> as format, for example:

variants <- get_smarter_variants(
  species = "Goat",
  assembly = "ARS1",
  query = list(
    region = "1:1-100000"
  )
)
Table continues below
affy_snp_id chip_name chrom date
Affx-1111832849 IlluminaGoatSNP50,AffymetrixAxiomGoatv2 1 2021-01-08
Affx-122941307 IlluminaGoatSNP50,AffymetrixAxiomGoatv2 1 2021-01-08
NA IlluminaGoatSNP50 1 2021-01-08
Table continues below
illumina illumina_strand illumina_top imported_from position strand
T/C BOT A/G manifest 18960 TOP
T/C BOT A/G manifest 47271 BOT
T/C BOT A/G manifest 63095 BOT
version name rs_id
ARS1 1_18960_AF-PAKI NULL
ARS1 snp14099-scaffold1560-920888 rs268246860
ARS1 GoatD01.029677 NULL

Fetch Variants by chip name

You can download all variants for a certain chip: please consider that it will require a lot of time and memory, since we store more than 600K SNPs in the smarter database. First, collect the available chips from the SMARTER-database, for example for the Sheep species:

sheep_chips <- get_smarter_supportedchips(query = list(species = "Sheep"))
manufacturer n_of_snps name species
illumina 54241 IlluminaOvineSNP50 Sheep
illumina 605998 IlluminaOvineHDSNP Sheep
affymetrix 56793 AffymetrixAxiomOviCan Sheep
affymetrix 49702 AffymetrixAxiomBGovisNP Sheep
affymetrix 60379 AffymetrixAxiomBGovis2 Sheep
NA 0 WholeGenomeSequencing Sheep

Then collect all the SNPs for a certain chip by providing the SMARTER chip name. Please, consider that you will download more than 50K SNP for this chip and this will take a lot of time

variants <- get_smarter_variants(
  species = "Sheep",
  assembly = "OAR3",
  query = list(
    chip_name = "IlluminaOvineSNP50"
  )
)