GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline

Frontiers in Genetics
Jose Afonso Guerra-AssuncaoJavier Herrero

Abstract

In recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole genome or whole exome sequencing, producing a genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalgenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the ...Continue Reading

References

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Datasets Mentioned

BETA
NA12878
PRJEB24961

Methods Mentioned

BETA
Human Genome Sequencing
exome sequencing
PCA
genotyping
RNAseq

Software Mentioned

PLINK
Nextflow
Open Humans
Docker
Open
UK
Ensembl Variant Effect Predictor
GATK
R
GenomeChronicler

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