Last updated: 2020-10-09

Checks: 1 1

Knit directory: NaCRRI_2020GS/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 7efdd90. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


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This repository and website documents all analyses, summary, tables and figures associated with NaCRRI genomic prediction and related procedures (e.g. imputation).

Imputation conducted in 2019

Imputation of the E. Africa reference panel and NaCRRI GS C2 (DArTseq only) was done in September 2019. The codes for 2019 imputation were never published in a Git repository, though they were shared internally. The 2019 imputed VCFs will serve as imputation reference panel for 2020. Therefore, I am publishing the 2019 codes here as is for reference.

“Imputation Reference Panel” consisted of 19,136 clones, includes samples in the W. Africa RefPanel except GS progeny. 413 clones (in addition to W. Africa dataset’s 411) were genotyped with both GBS and DArTseqLD (~340 from TARI). 56,250 SNP (imputed, phased and filtered). The East Africa version of the RefPanel was used to impute 1597 samples (NaCRRI GS C2) genotyped with DArTseq (not DArTseqLD). The resulting dataset after keeping only sites passing post-impute filters for the progeny has 23,431 SNP (“ready for GS”).

Found here: ftp://ftp.cassavabase.org/marnin_datasets/nextgenImputation2019/ImputationEastAfrica_StageIII_91119/

E.g. chr1_ImputationEastAfrica_AllSamples_ReadyForGP_91419.vcf.gz

Two DArT reports were involved:

DArT reports involved:

  1. DCas19_4459: Tanzania samples with DArTseqLD, NaCRRI samples with DArTseq (not LD).
  2. DCas19_4432: NaCRRI GS C2 (DArTseq not LD).

Steps:

Imputation conducted in 2020

DArTseqLD (DCas20-5419) arrived in September 2020. From Robert Kawuki: From Robert Kawuki on Sep 1, 2020: “These samples were derived from Pre-breeding populations we have. On cassavabase under the NaCRRI folder these applies to populations namely”2019_SET_Pre_Breeding_Namulonge" and “2019_CET_Pre_Breeding_Namulonge”. These populations comprise crosses made between East African clones with Latin American and/or West African clones."

Steps:

Since imputation with Beagle5.0 is very fast, and given the origins of the samples, I’d like to impute it a few different ways and allow NaCRRI team to compare and contrast in downstream analysis.

Specifically, I think it makes sense to impute it with variants of the reference panel: (1) E. Africa ref panel, (2) L. America.

  1. E. Africa ref panel
  1. L. America ref panel

SUGGESTION: Use combination PCA, prediction, correlation of kinship matrices (off-diagonals and diagonals) to compare these datasets.

Genomic prediction in 2020

None as yet.

Data availability and reproducibility

The R package workflowr was used to document this study reproducibly.

Much of the supporting data and output from the analyses documented here are too large for GitHub.

The repository will be mirrored, here: ftp://ftp.cassavabase.org/marnin_datasets/NaCRRI_2020GS/ with all data.

Directory structure of this repository

NOTICE: data/ and output/ are empty on GitHub. Please see ftp://ftp.cassavabase.org/marnin_datasets/NaCRRI_2020GS/ for access.

  1. data/: raw data (e.g. unimputed SNP data)
  2. output/: outputs (e.g. imputed SNP data)
  3. analysis/: most code and workflow documented in .Rmd files
  4. docs/: compiled .html, “knitted” from .Rmd

Supporting functions code/

The analyses in the html / Rmd files referenced above often source R scripts in the code/ sub-folder.

Further details on imputation procedure

The common strategy for imputation used across all imputations in 2019 is as follows:

Relies on:

  1. Samples genotyping with both marker platforms (GBS + DArT)

  2. SNP markers observed by both platforms

  3. NextGenC custom DArT assay and reporting format, namely use of the ApeKI restriction enzyme _and_ reporting of read depth data to us.

  4. Read depth data was used to compute genotype likelihoods (GL). For imputation, I used a combination of Beagle4.1 to do initial imputation steps. Beagle 4.1 is slow _but_ can use the GLs to produce a result which should be more accurate than simply using called genotypes (GT). For phasing steps _and_ for the imputation of target progeny (those with DArT-only), I used Beagle5.0 because it is _fast_ and _accurate_ IF you have GT calls and a big reference panel.

  5. Be conservative. Between each imputation step, I applied the following filter: keep sites with AR2 or DR2>=0.75, P_HWE>1e-20, MAF>0.005. AR2 and DR2 are scores assigned by Beagle4.1 and Beagle5.0, respectively to measure expected quality of imputation (reported in the INFO field of VCF). P_HWE was based on HWE chi-square done by `vcftools`. MAF>0.005 is to remove anything that is essentially fixed in the dataset.

  6. Samples that were supposed to have GBS and DArT were verified before combining the data. Used identity-by-descent (IBD) estimation in plink v1.9 (`plink1.9 –genome`) at DArT-GBS intersecting sites, to validate identity match (threshold >=0.75).

Two stages to building imputation reference panels:

Stage I. Impute all GBS+DArT samples. Plus GBS-only founders and diversity lines.

Stage II. Impute GBS-only GS descendents

Third and final Stage III: Impute target panels (i.e. selection candidates with DArT-only).