Pv1: Plasmodium vivax Genome Variation Project (May 2016 data release)

Through an analysis of 228 parasite samples collected in 13 different countries, we identified 704,710 biallelic single nucleotide polymorphisms (SNPs). This download includes genotyping data for samples contributed to the MalariaGEN Plasmodium vivax Genome Variation Project.

Genotyping data is currently released for all identified biallelic single nucleotide polymorphisms (SNPs). Most subsequent analyses were performed on a subset of 303,616 SNPs which were selected by multiple quality filtering procedures, aimed at reducing the number of false positives. These high-quality SNPs can be identified by the string PASS in the FILTER column of the VCF file and represent the set of variations that we feel most confident to genotype.

The methods used to generate the data are described in detail in Genomic analysis of local variation and recent evolution in Plasmodium vivax, Nature Genetics, 2016 (dx.doi.org/10.1038/ng.3599).

The sequence data were generated by the Wellcome Trust Sanger Institute as part of the P. vivax Genome Variation, an international collaboration involving several independent research groups. These data are described in Pearson et al, 2016.

If you use these data, we expect you to respect the efforts of data producers by citing the source of the data. If your analyses result in a publication, please include the following acknowledgement in your Methods section: "This publication uses data from the MalariaGEN P. vivax Genome Variation project, as described in Pearson et al, Nature Genetics, 2016 (dx.doi.org/10.1038/ng.3599)."

Additionally, you may also cite the data set directly: MalariaGEN P. vivax Genome Variation project (2016). P. vivax Genome Variation May 2016 data release. MalariaGEN. 

File descriptions:

PvGV_May2016_sample_data.xlsx: Sample metadata including ENA accessions numbers, country and year of collection, partner study information, and sample IDs for 228 samples from 13 countries.

pv_1_0_NG_manuscript.vcf.gz: The data file ("*.vcf.gz") is a zipped VCF format file containing all samplesin the study. 

pv_1_0_NG_manuscript.vcf.gz.tbi: This is a tabix index file for pv_1_0_NG_manuscript.vcf.gz

README.txt: contains further tips and tricks for accessing data in the VCF file