EMBRAPA 2020 GS and related procedures

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Last updated: 2020-10-17

Checks: 7 0

Knit directory: EMBRAPA_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.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200826)

The command set.seed(20200826) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

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Repository version: 58815fb

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 58815fb. 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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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	58815fb	wolfemd	2020-10-17	More tweaks!
html	4126297	wolfemd	2020-10-17	Build site.
Rmd	686ad48	wolfemd	2020-10-17	More tweaks!
html	a1779c2	wolfemd	2020-10-17	Build site.
Rmd	dfde5bc	wolfemd	2020-10-17	More tweaks!
html	972bc9a	wolfemd	2020-10-17	Build site.
Rmd	20aef71	wolfemd	2020-10-17	Tweaks to bulleted lists.
html	45cee36	wolfemd	2020-10-17	Build site.
Rmd	f309dea	wolfemd	2020-10-17	Start workflowr project.
html	fa3b6e1	wolfemd	2020-09-01	Build site.
html	d97980a	wolfemd	2020-09-01	Build site.
Rmd	f3a0e16	wolfemd	2020-09-01	Added a link to cassavabase FTP destination for the data.
html	d29d605	wolfemd	2020-09-01	Build site.
Rmd	6e27397	wolfemd	2020-09-01	EMBRAPA C2 has been imputed. Publish report and share to cassavabase
html	ed70a5a	wolfemd	2020-08-26	Build site.
Rmd	9d4dfab	wolfemd	2020-08-26	Code organized into functions. Ready to run imputation of C2?
Rmd	4cc20db	wolfemd	2020-08-26	Start workflowr project.
Rmd	245ee4f	wolfemd	2020-08-26	Start workflowr project.

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

Imputation 2019

Imputation conducted in 2019: Imputation of the L. America reference panel (GBS+DArTseqLD) and EMBRAPA GS C1 (DArTseqLD only) was done in October 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.

• Convert DCas19-4403 report to VCF for imputation: The report DCas19_4403 was converted to VCF and then included in the ImputationReferencePanel VCF and imputed along with the GBS/GBS+DArT samples.
• Verify GBS-to-DArTseqLD sample matches: Verify GBS-2-DArT matches by PLINK IBD was done on samples DCas19_4301.
• Imputation steps: this was a multi-stage process including assembly and filtering of VCFs, imputation with Beagle (4.1 and 5.0). The ultimate step of this pipeline was to impute the C1 progeny data, which were extracted from the DArTseqLD report “DCas19_4301”, with the imputation reference panel.

Imputation 2020

DArTseqLD (DCas20-5360) arrived on Aug. 22, 2020. Contains GS C2 for EMBRAPA.

STEPS:

• Convert DCas20-5360 report to VCF for imputation:

• Impute DCas20-5360:

  • NEW SECTION: Dosage format files, see below for guide to files.
  • NEW SECTION: Less stringent filter (DR2>0.3), see below for guide to files.

FILES:

DOWNLOAD FROM CASSAVABASE FTP SERVER orDOWNLOAD (files <50Mb) FROM GitHub

Last year’s reference panel for imputation had ~64K SNP. The C1 progeny imputed by it had <9K SNP after post-imputation filters. Since imputation with Beagle5.0 is very fast, I imputed C2 (DCas20-5360) with three variants of the reference panel:

1. Last year’s reference panel, without C1 (64K SNP)

• RefPanel VCF filename: chr*_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz

• Imputed C2 filename: chr*_DCas20_5360_REFimputed.vcf.gz

• Post-impute filtered C2 filename: chr*_DCas20_5360_REFimputedAndFiltered.vcf.gz

• Genome-wide dosage matrix format for use in R:

  • Imputation Reference Panel: DosageMatrix_ImputationReferencePanel_EMBRAPA_Phased_102619.rds

  • DCas20_5360 with standard post-impute filter: DosageMatrix_DCas20_5360_REFimputedAndFiltered.rds

  • DCas20_5360 with “light” post-impute filter: DosageMatrix_DCas20_5360_REFimputeLightFiltDR2pt3.rds

2. Last year’s ref. panel + C1 (include unfiltered C1 data = 64K refpanel SNP)

• RefPanel VCF filename: chr*_ImputationReferencePanel_C1progenyAdded_EMBRAPA.vcf.gz

• Imputed C2 filename: chr*_DCas20_5360_REFimputedWithC1unfiltered.vcf.gz

• Post-impute filtered C2 filename: chr*_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered.vcf.gz

• Genome-wide dosage matrix format for use in R:

  • Imputation Reference Panel: DosageMatrix_ImputationReferencePanel_C1progenyAdded_EMBRAPA.rds

  • DCas20_5360 with standard post-impute filter: [WARNING: 0 SNP on Chr. 4] DosageMatrix_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered.rds

  • DCas20_5360 with “light” post-impute filter: [WARNING: 0 SNP on Chr. 4] DosageMartix_DCas20_5360_REFimputedWithC1unfiltered_LightPostImputeFiltDR2pt3.rds

• NOTICE: REFimputedWithC1unfiltered is not a good dataset. Chr. 4 is entirely filtered out, including using the “lighter” filter. This emphasizes that it is not a good idea to use poorly imputed haplotypes in the reference panel… evidenced also by the fact that the REFimputedWithC1filtered has markers passing filters on all chromosomes.

3. Last year’s reference panel + C1 (reduce refpanel to sites passing post-impute filter in C1 = 9K SNP)

• RefPanel VCF filename: chr*_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA.vcf.gz

• Imputed C2 filename: chr*_DCas20_5360_REFimputedWithC1filtered.vcf.gz

• Post-impute filtered C2 filename: chr*_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered.vcf.gz

• Genome-wide dosage matrix format for use in R:

  • Imputation Reference Panel: DosageMatrix_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA.rds

  • DCas20_5360 with standard post-impute filter: DosageMatrix_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered.rds

  • DCas20_5360 with “light” post-impute filter: DosageMartix_DCas20_5360_REFimputedWithC1filtered_LightPostImputeFiltDR2pt3.rds

HOW TO COMBINE DOSAGE MATRICES: Users will want to combine the genotypes in the imputation reference panel files, with the genotypes in the imputed DArT file. They can have slightly different sets of markers along the columns. Here is a basic example how to combine:

snps_refpanel<-readRDS("DosageMatrix_ImputationReferencePanel_EMBRAPA_Phased_102619.rds")
snps_dcas20_5360<-readRDS("DosageMatrix_DCas20_5360_REFimputeLightFiltDR2pt3.rds")

snps2keep<-colnames(snps_refpanel)[,colnames(snps_refpanel) %in% colnames(snps_dcas20_5360)]
snps<-bind_rows(snps_refpanel[,snps2keep],
                snps_dcas20_5360[,snps2keep])

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

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/EMBRAPA_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/EMBRAPA_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. These are wrapper functions around the packaged core functions in predCrossVar, to do the specific analyses for this paper.

Session information

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5       whisker_0.4      knitr_1.30       magrittr_1.5    
 [5] R6_2.4.1         rlang_0.4.8      stringr_1.4.0    tools_4.0.2     
 [9] xfun_0.18        git2r_0.27.1     htmltools_0.5.0  ellipsis_0.3.1  
[13] yaml_2.2.1       digest_0.6.25    rprojroot_1.3-2  tibble_3.0.4    
[17] lifecycle_0.2.0  crayon_1.3.4     later_1.1.0.1    vctrs_0.3.4     
[21] promises_1.1.1   fs_1.5.0         glue_1.4.2       evaluate_0.14   
[25] rmarkdown_2.4    stringi_1.5.3    compiler_4.0.2   pillar_1.4.6    
[29] backports_1.1.10 httpuv_1.5.4     pkgconfig_2.0.3