SPORE will take as input a VCF file of a population and will output a pedigree based on the genotypes in the VCF file. However, only parent-offspring relationships will be inferred. The difference of SPORE to other methods is that it works well in very inbred populations. A manuscript detailing the method can be found here: https://www.biorxiv.org/content/10.1101/2021.11.23.469656v2.
You must be reasonably sure that there is at least one parents-offspring trio among the individuals in the VCF as that SPORE assumes this and will deliver false results if this assumption is not met.
You need about 10,000 loci per chromosome for IBD0 IQR calculation, otherwise (if you disable IBD0 IQR calculation), you only need about 10,000 loci for IBD0 calculation or theoretically no minimum (though this is not tested) if you disable IBD0 and IBD0 IQR calculation (thus only relying on homozygous and Mendelian trio mismatches).
You will likely need a Unix-based operating system (Linux) to fulfill the prerequisites for the script, especially for TRUFFLE. If you opt not to use TRUFFLE for IBD calculation (by providing your own IBD data as input), then the script may run not just on Linux, but this was not tested, so should only be done by folks with more experience. Similarly, on Windows you can probably get away with using the Ubuntu shell installation that is possible since Windows 10.
Tested with beta 1.38.
Available at https://adimitromanolakis.github.io/truffle-website/.
To use the script, simply make sure you have all the prerequisites mentioned above and below, clone this repository, and edit the SPORE-Settings.R file to suit your needs.
The easiest way to meet the prerequisites (except for TRUFFLE, see above) is to create an anaconda environment (https://www.anaconda.com/products/distribution), ideally with mamba (https://mamba.readthedocs.io/en/latest/) for faster speed, but you can write conda instead of mamba if you don't have it installed.
mamba create -n SPORE r-base=3.6.3 r-readr=1.4.0 r-stringr=1.4.0 r-dplyr=1.0.2 r-tidyr=1.1.2 r-data.table=1.13.2 r-ggplot2=3.3.2 r-naturalsort=0.1.3 r-sys=3.4 r-r.utils gzip bcftools=1.10 git
conda activate SPORE
git clone https://github.com/jnrunge/SPORE.git
and you can see if it runs using the example data (after having adjusted the path to truffle in the example configuration file example_data/SPORE-Settings-for-example_data.R).
cd SPORE/example_data
Rscript ../SPORE.R SPORE-Settings-for-example_data.R
You can then compare results with md5sum -c results/md5.txt.
Tested with 1.10.
Available here: https://github.com/samtools/bcftools
The script requires R with some packages installed. The versions with which the script was tested are listed below.
SPORE was tested with / written for:
- R 3.6.3
- readr 1.4.0
- stringr 1.4.0
- dplyr 1.0.2
- tidyr 1.1.2
- data.table 1.13.2
- ggplot2 3.3.2
- naturalsort 0.1.3
- sys 3.4
- this.path 0.4.4
- R.utils
Please edit the configuration in SPORE-Settings.R and follow the descriptions in there.
Execute the script (after configuration) with the command
RScript SPORE.R SPORE-Settings.R- Individual names should not include underscores "_".
*-imputed_pedigree.ped This is the main result file and includes the pedigree as SPORE was able to infer it. If you input sexes, then "Father" and "Mother" columns are used, otherwise "ParentSexQ1" and "ParentSexQ2" will still contain trio results. If samples were very similar genetically (by default, IBD2
*-PO-undirected.tsv This contains a list of relationships where ID1 and ID2 were detected as parent and offspring, but could not be 'directed', meaning that it is unclear who is parent and who is offspring.
*-trios-choices.csv Table detailing the different choices SPORE made when multiple trios where possible for a given individuals.
*-IBD0_threshold.png This shows a plot where on the x axis are different thresholds of IBD0 and the y gives the fraction for three different variables: in blue, how many individuals have at least one relationship with another individual below the IBD0 threshold; in red, how many individuals have more than when_PO_error relationships (see configuration file); and in black the distance between those two fractions. The black dot highlights the maximum value of the black line, which is also written on the top left, and was subsequently used as a threshold by SPORE.
*-IBD0_IQR_threshold.png Same as above, but for the inter-quartile range of IBD0 between the chromosomes.
*-homo_mendel_rel_threshold.png Same as above, but for the fraction of the genome that contains incompatible homozygous genotypes (e.g. 0/0 and 1/1) for two focals.
*-TrioMendelErrorsComparedToMeanThreshold.png Similar to before, but here we show on the x a threshold of how a trio's Mendelian errors compare to the mean Mendelian errors of all trios. In blue we show focals with exactly one trio that is below that threshold and in red focals with more than 1 trio below the threshold. The threshold is then picked (blue dot) based on the highest fraction of focals that have exactly one trio.
*-TrioMendelErrorsPercentileThreshold.png Same as above, but the x is the percentile of Mendelian errors within all trios that were looked at for a given focal.
*_threshold.csv.gz The data that generated the plots for further analyses if desired.
*_threshold.txt The threshold calculated, so that re-calculation can be skipped if desired.