Ethnicity Annotation from Whole Exome Sequencing Data

Reliable and rapid ethnicity annotation from whole exome sequencing data.


= EthSEQ News

== Changes in EthSEQ 2.1.2

  • When running ethseq.Analysis with a VCF input file, intersection of variants in the VCF and reference model are computed and used to perform the analysis.

== Changes in EthSEQ 2.1.1

  • Added parameter "bam.chr.encoding" to specify that input BAM files have chromosomes encoded with prefix "chr"
  • Prefix "chr" of chromosome names (when present) in VCF input target models are now automatically deleted
  • Reference models with ethseq.RM are now created deleting prefix "chr" from chromosome names (when present) in VCF input files

== Changes in EthSEQ 2.1.0

  • First 3 PCA components can now be used to perform ethnicity analysis. Parameter "space" in ethseq.Analysis function can now be used to specificy the analysis mode ("3D" or default "2D").
  • Added reference models with mixed american population (AMR) as defined by 1,000 Genome Project data. Models name containing the label "Major" are built from EUR, AFR, SAS and EAS populations data (1,000 Genome Project genotype data), while models containing label "All" are built considering in addition AMR population. List of current available reference models is: ..* HALO.All.gsd and HALO.Major.gds (SNPs in Haloplex) ..* SS2.All.gsd and SS2.Major.gds (SNPs in Sure Select v2) ..* SS4.All.gsd and SS4.Major.gds (SNPs in Sure Select v4) ..* NimblegenV3.All.gsd and NimblegenV3.Major.gds (SNPS in Nimblegen SeqCap EZ Exome v3) ..* Exonic.All.gsd and Exonic.Major.gds (SNPS in all exonic regions as per GENCODE v14)
  • For individuals with multiple ethnicity annotations (e.g. "EUR|SAS") the contribution of all reference populations is reported as percentage value
  • Check existence of BAM files defined in the input BAM file list
  • When a reference model is created a VCF file with all SNPs selected to build the reference GDS model is reported (file named "Filtered_SNPs.vcf")

Reference manual

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2.1.2 by Alessandro Romanel, a year ago

Browse source code at

Authors: Alessandro Romanel

Documentation:   PDF Manual  

GPL-3 license

Imports graphics, utils, parallel, grDevices, MASS, geometry, data.table, SNPRelate, gdsfmt, plot3D

Suggests knitr, rmarkdown

See at CRAN