Program parameters and options

Mostly used

-vcf [file] File path of the isolate vcf. Assume all variants are PASS in the QUAL column, the VCF file also reqires the AD field.

Note: In the current implementation, DEploid only take the first sample in the VCF file. DEploid DO NOT handle multi-allelic variants, nor indels. The FILTER column will not be used.
-plaf [file] File path of population level allele frequencies (tab-delimited plain text file), for example

CHROM POS PLAF

Pf3D7_01_v3 93157 0.0190612159917058

Pf3D7_01_v3 94422 0.135502358766423

Pf3D7_01_v3 94459 0.156294363760064

Pf3D7_01_v3 94487 0.143439298925837
-panel [file] File path of the reference panel (tab-delimited plain text file), for example

CHROM POS 3D7 Dd2 Hb3 7G8

Pf3D7_01_v3 93157 0 0 0 1

Pf3D7_01_v3 94422 0 0 0 1

Pf3D7_01_v3 94459 0 0 0 1

Pf3D7_01_v3 94487 0 0 0 1
-noPanel Use population level allele frequency as prior.

Warning: Flags -panel and -noPanel should not be used together.
‘-exclude [file]’ File path of sites to be excluded (tab-delimited plain text file).
‘-o [string]’ Specify the file name prefix of the output.
‘-k [int]’ Number of strain (default value 5).
‘-nSample [int]’ Number of MCMC samples (default value 800).
‘-rate [int]’ MCMC sample rate (default value 5).
‘-burn [float]’ MCMC burn rate (default value 0.5).
‘-v , -version’ DEploid version.
‘-vcfOut’ Save final halpotypes into a VCF file.

CHROM	POS	PLAF
Pf3D7_01_v3	93157	0.0190612159917058
Pf3D7_01_v3	94422	0.135502358766423
Pf3D7_01_v3	94459	0.156294363760064
Pf3D7_01_v3	94487	0.143439298925837

CHROM	POS	7G8
Pf3D7_01_v3	93157	1
Pf3D7_01_v3	94422	1
Pf3D7_01_v3	94459	1
Pf3D7_01_v3	94487	1

You may also try

‘-ref [file] -alt [file]’ File path of reference and alternative allele count (tab-delimited plain text file).

Note: In early dEploid versions (prior to v0.2-release), allele counts extracted from the vcf file are placed in two files, and parsed by flags -ref [file] and -alt [file]. Tab-delimited plain text for input. First and second columns record chromosome and position labels respectively. Third columns records the reference allele count or alternative allele count. For example,

CHROM POS PG0390.C

Pf3D7_01_v3 93157 85

Pf3D7_01_v3 94422 77

Pf3D7_01_v3 94459 90

Pf3D7_01_v3 94487 79

CHROM POS PG0390.C

Pf3D7_01_v3 93157 0

Pf3D7_01_v3 94422 0

Pf3D7_01_v3 94459 0

Pf3D7_01_v3 94487 0

Warning: Flags -ref and -alt should not be used with -vcf.
-forbidUpdateProp Forbid MCMC moves to update proportions.
-forbidUpdateSingle Forbid MCMC moves to update single haplotype.
-forbidUpdatePair Forbid MCMC moves to update pair haplotypes.
-exportPostProb Save the posterior probabilities of the final iteration of all strains.
-miss [float] Miss copying probability
-recomb [float] Constant recombination probability
-initialP [float ...] Initialize proportions.
-p [int] Output precision (default value 8).

CHROM	POS	PG0390.C
Pf3D7_01_v3	93157	85
Pf3D7_01_v3	94422	77
Pf3D7_01_v3	94459	90
Pf3D7_01_v3	94487	79

CHROM	POS	PG0390.C
Pf3D7_01_v3	93157	0
Pf3D7_01_v3	94422	0
Pf3D7_01_v3	94459	0
Pf3D7_01_v3	94487	0

Example

Data exploration, plot the read count ALT vs REF.

library(DEploid)

vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390 = extractCoverageFromVcf(vcfFile)
plotAltVsRef( PG0390$refCount, PG0390$altCount )

Plot the histogram of the observed allele frequency within sample.

obsWSAF = computeObsWSAF( PG0390$altCount, PG0390$refCount )
histWSAF(obsWSAF)

Load prior information: PLAF and reference panel

plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
plaf = extractPLAF(plafFile)
panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")

Deconvolute the haplotypes

set.seed(1)
PG0390.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-panel", panelFile))
prop = PG0390.deconv$Proportions[dim(PG0390.deconv$Proportions)[1],]
expWSAF = t(PG0390.deconv$Haps) %*% prop

Plot the allele frequency within sample (observed in red, expected in blue) against the population level allele frequency.

plotWSAFvsPLAF(plaf, obsWSAF, expWSAF)

Plot the history of the MCMC proportion estimates.

plotProportions(PG0390.deconv$Proportions)

Plot the allele frequency within sample, observed against expected.

plotObsExpWSAF(obsWSAF, expWSAF)

Reporting Bugs

If you encounter any problem when using dEploid, please file a short bug report by using the issue tracker on GitHub or email joe.zhu (at) well.ox.ac.uk.

Please include the output of dEploid -v and the platform you are using dEploid on in the report. If the problem occurs while executing dEploid, please also include the command you are using and the random seed.

Thank you!

Citing DEploid

If you use dEploid with the flag -ibd, please cite the following paper:

Zhu, J. S., J. A. Hendry, J. Almagro-Garcia, R. D. Pearson, R. Amato, A. Miles, D. J. Weiss, T. C. D. Lucas, M. Nguyen, P. W. Gething, D. Kwiatkowski, G. McVean, and for the Pf3k Project. (2018) The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria. eLife, 40845, doi: https://doi.org/10.7554/eLife.40845.

If you use dEploid in your work, please cite the program:

Zhu, J. S., J. A. Garcia, G. McVean. (2018) Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. Bioinformatics 34(1), 9-15. doi: https://doi.org/10.1093/bioinformatics/btx530.

Bibtex record::

@article {Zhu387266, author = {Zhu, Sha Joe and Hendry, Jason A. and Almagro-Garcia, Jacob and Pearson, Richard D. and Amato, Roberto and Miles, Alistair and Weiss, Daniel J. and Lucas, Tim C.D. and Nguyen, Michele and Gething, Peter W. and Kwiatkowski, Dominic and McVean, Gil and ,}, title = {The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria}, year = {2018}, doi = {10.1101/387266}, publisher = {Cold Spring Harbor Laboratory}, URL = {https://www.biorxiv.org/content/early/2018/08/09/387266}, eprint = {https://www.biorxiv.org/content/early/2018/08/09/387266.full.pdf}, journal = {bioRxiv} }

@article {Zhubtx530, author = {Zhu, Sha Joe and Almagro-Garcia, Jacob and McVean, Gil}, title = {Deconvolution of multiple infections in {{}} from high throughput sequencing data}, year = {2017}, doi = {10.1093/bioinformatics/btx530}, URL = {https://doi.org/10.1093/bioinformatics/btx530}, journal = {Bioinformatics} }

Command Line Arguments

Sha Zhu

2020-04-21