CGIAR Genomics

This R package was designed to facilitate the reading, filtering and post-processing of genetic data of diploid and polyploid bi-allelic single nucleotide polymorphisms (SNP) makers. The software has been developed and tested with data from CGIAR research centers.

Installation

install.packages("devtools")
library(devtools)
install_github("Breeding-Analytics/cgiarGenomics")
library(cgiarGenomics)

Data preparation

The user has the option of load the genotypic information using the following formats:

• Hapmap (diploid & polyploid support)
• VCF (diploid & polyploid support)
• DartSeq SNP (only diploid support)
• DartTag (counts and dosage file)

Genotype reading process

On its core the package wants to convert the marker data into an genlight instance. This because genlight internally codes chunks of 8 SNPs using a single byte, resulting in drastic compression of the data. Support any ploidity level.

To perform the instantiation of a genlight object its necessary provide the allelic dosage matrix of only bi-allelic SNPs for this reason is necessary first filter all the variants that doesn't meet this requierment. For doing so, is mandatory the allelic information (ref and alt alleles) and the physical position (Chromosome, position). Here a general flowchart of the reading process.

flowchart LR
    A["Genotype Data"] --> B["Extract Metadata \n (ID, CHR, POS, REF, ALT)"]
    B --> C["Flag markers with \n incomplete and duplicated physical position"]
    C --> D["Flag markers with \n duplicated id"]
    D --> E["Flag markers with \n no data at REF and ALT"]
    E --> F["Flag markers where \n REF or ALT don't meet ^ACGT$ (only snps)"]

Loading

Flaged markers are removed and are kept only the bi-allelic snps and here is the flowchart to get the dosage matrix to produce the genlight instance:

flowchart LR
    A["Given the alleles \n of the marker get all possible genotype calls"] --> B["Given the ALT allele in metadata \n get the dosage of possible genotype calls"] 
    B --> C["Replace the calls of the \n marker with assigned dosage"] 
    C --> D["Create the genlight instance"]

Loading

Hapmap

Use the following examples to format your hapmap file.

Code Meaning

A Adenine C Cytosine G Guanine T Thymine

Diploid example

rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panelLSID	QCcode	sample_1
44509	A/G	Chr02	5565755	NA	NA	NA	NA	NA	NA	NA	AG

Tetraploid example

rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panelLSID	QCcode	sample_1
44509	A/G	Chr02	5565755	NA	NA	NA	NA	NA	NA	NA	AAGG

Notes

The alleles column should always be separated with "/"

VCF

Diploid example

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1
Chr01	120931	S1_120931	C	A	.	PASS	AC=25;AN=1560	GT	0/0

Tetraploid example

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1
Chr01	510745	solcap_snp_c2_36615	T	G	.	.	NS=367;DP.AVG=65.6;AF=0.26	GT:AD:DP	0/0/0/1:47,9:56

DArT Seq SNP

Standard DArT Seq SNPs format delivered by Diversity arrays. We use the DartR function named gl.read.dart to load those files.

DArT Tag (Polyploid)

Two files are expected, counts.file and dosage file. We use the function dart2vcf of polyBreedR package.