Nextflow pipeline that runs and plots admixture and smartpca from a compressed VCF.
-v 0.0.1
- Supports vcf compressed files as input.
- Results include PCA plot, PCP plot and admixture plots.
- Parameters of smartpca and admixture could be changed in Nextflow config.
- Scalability and reproducibility via a Nextflow-based framework.
* VCF2PCP may run in other UNIX based OS and versions, but testing is required.
| Requirement | Version | Required Commands * |
|---|---|---|
| bcftools | 1.9-220-gc65ba41 | bcftools |
| plink | 2 | plink |
| Eigensoft | 6.1.4 | smartpca |
| Admixture | 1.3 | admixture |
| Nextflow | 19.04.1.5072 | nextflow |
| Plan9 port | Latest (as of 10/01/2019 ) | mk ** |
| R | 3.4.4 | ** See R scripts |
* These commands must be accessible from your $PATH (i.e. you should be able to invoke them from your command line).
** Plan9 port builds many binaries, but you ONLY need the mk utility to be accessible from your command line.
Download VCF2PCP from Github repository:
git clone https://github.com/jbv2/VCF2PCP.git
To test VCF2PCP execution using test data, run:
./runtest.sh
Your console should print the Nextflow log for the run, once every process has been submitted, the following message will appear:
```
======
vcf2pcp: Basic pipeline TEST SUCCESSFUL
======
```
VCF2PCP results for test data should be in the following file:
VCF2PCP/test/results/VCF2PCP-results
To run VCF2PCP go to the pipeline directory and execute:
nextflow run vcf2pcp.nf --vcffile <path to input 1> [--output_dir path to results ]
For information about options and parameters, run:
nextflow run vcf2pcp.nf --help
- A compressed vcf file with extension '.vcf.gz'. Example line(s):
##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO
chr21 5101724 . G A . PASS AC=1;AF=0.00641;AN=152;DP=903;ANN=A|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19987C>T|||||||||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5101724G>A||||||||||||||||||||||||||||2.079|0.034663||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
chr21 5102165 rs1373489291 G T . PASS AC=1;AF=0.00641;AN=140;DP=853;ANN=T|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19546C>A|||||||rs1373489291||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5102165G>T||||||||||||||||||||||||||||5.009|0.275409||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
- A file that contains name of samples and the group that belongs to, separated by " ".
(samples.txt)
Example line(s):
sample1 Zoque
sample2 PEL
sample3 PEL
sample4 CHB
...
- A file that contains sample, pop and region separated by tabs.
(tag_data.tsv). It helps for regions like north, central and south.
Example line(s):
sample pop region
sample2 PEL PEL
sample3 PEL PEL
sample4 CHB CHB
...
- best snps
- Tracy-Widom statistics
- std out
- PCP of first 20 PCs. This also says which is the last significant PC and variance explained by them.
- Plot of PCA1 vs each PC(2:20).
- PCP by region with first 20 PCs.
- kmeans plot.
- tsv and plot of CVS which shows the minor Crossvalidation value.
- admixture plots from k 2:9 separated and all together.
VCF2PCP
├── dev_notes ## Developers notes directory
│ └── Workflow.png ## Flow diagram
├── mkmodules ## Directory for submodule organization
│ ├── mk-gather-admixture-plots ## Submodule to gather admixture plots.
│ ├── mk-keep-autosomes ## Submodule to select only autosomal chromosomes.
│ ├── mk-k-means-analysis ## Submodule to do kmeans analysis.
│ ├── mk-make-par-file_smartpca ## Submodule to run smartpca.
│ ├── mk-make-pedind ## Submodule to make pedind file.
│ ├── mk-make-pop-info ## Submodule to make popinfo file.
│ ├── mk-parallel_coordinate_plot ## Submodule to make PCP.
│ ├── mk-plot-admixture ## Submodule to plot admixture results.
│ ├── mk-plot-cvs ## Submodule to plot cvs of admixture.
│ ├── mk-regional-PCA ## Submodule to perform regional PCA.
│ ├── mk-rejoin-vcf ## Submodule to rejoin vcf chunks.
│ ├── mk-run-admixture ## Submodule to run admixture.
│ ├── mk-simplifyVCF-removeLD ## Submodule to format vcf.
│ ├── mk-split-chromosomes ## Submodule to split chromosomes.
│ └── mk-vcf2PLINK ## Submodule to convert vcf to plink
├── nextflow.config ## Configuration file for this pipeline.
├── README.md ## This document. General workflow description
├── runtest.sh ## Execution script for pipeline testing.
├── test ## Test directory.
│ ├── data ## Test data directory
│ └── reference ## Test reference directory
└── vcf2pcp.nf ## Flow control script of this pipeline.
Under the hood nf-vcf-novel-dataset-builder uses some coding tools, please include the following ciations in your work:
- Narasimhan, V., Danecek, P., Scally, A., Xue, Y., Tyler-Smith, C., & Durbin, R. (2016). BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics, 32(11), 1749-1751.
- Team, R. C. (2017). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http s. www. R-proje ct. org.
- Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.
- D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.
- Price, Alkes L., et al. "Principal components analysis corrects for stratification in genome-wide association studies." Nature genetics 38.8 (2006): 904-909.
- Patterson, Nick, Alkes L. Price, and David Reich. "Population structure and eigenanalysis." PLoS genetics 2.12 (2006): e190.
If you have questions, requests, or bugs to report, please email judith.vballesteros@gmail.com or iaguilaror@gmail.com
Judith Ballesteros Villascán judith.vballesteros@gmail.com
Israel Aguilar-Ordonez iaguilaror@gmail.com
Fernando Pérez-Villatoro frpvillatoro@gmail.com
If you find this pipeline useful for your project, please cite us as:
Aguilar-Ordoñez, Israel, et al. "Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights." PloS one 16.4 (2021): e0249773.