Analyzing and identifying genomic variants is particularly helpful in case of linking the disease onset to the genomic predictions. Genomic variants play a key role in the identifcation and characterization of the disease onset and also allow for interlinking genomic variability and hypothesis testing. eVai, which is a variant annotation platform provides annotation of the genomic variants using several backhand open source databases and tools. eVaiutilities proposed in this paper, is a data management software for the analysis of the eVai output files. It allows the analysis of the genomic variants further such as analyzing the multiple genomic anntoated variants, reference and alternate allele, enabling cocordinate search, coordinate search with specificed variants and annotation search across a large number of population. The availability of the command line parameters allows for a large scale analysis across the several population files.
- eVai-utilities for data management of the eVai results. It supports all versions of eVai.
- It analyzes the eVai output files for variant annotation to filtering, preparating user reports and database and annotator and more. See the example folder for the older and the newer version files.
- It provides the population scale variant searching given a folder according to the variant, annotation, transcript, gene, and coordinates.
cargo build
annotating and analyzing eVai results.
************************************************
Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: [email protected]
Funded through Development of a universal fast-response platform,
based on RNA technology,ensuring the national drug and epidemiological safety.
2021/ABM/05/00004-00 to
Prof. Luiza Handschuh: [email protected].
*************************************************
Usage: eVaiutilities <COMMAND>
Commands:
variant-analyzer analyzer for the variants
variant-filter filter the variants
variant-database create variant database
gtf-analyze analyze the corresponding gtf
variant-seq prepare the variant seq annotation
download-genome download the human genome
acmg-transcript variant-transcriptids
sequence-profile sequence profiling
population-variant-search search for the variant across population
coordinate-search search according to coordinates
coordinate-search-variant search according to coordinates and variant
annotation-search search according to annotation
pathogenicity-filter pathogenicity filter
population-variant-searcholder search for the variant across population older version
coordinate-searcholder search according to coordinates older version
coordinate-searc-variantholder search according to coordinates and variant older version
annotation-searcholder search according to annotation older version
pathogenicity-filterolder pathogenicity filter older version
transcript-search search by the specific transcript
transcript-searcholder search by the specific transcript older
alt-allele search for the ref allele
alt-ref-allele search according to ref allele and alt allele
alt-allele-older search for the ref allele older version
alt-ref-allele-older search according to ref allele and alt allele older version
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
variant-analyzer ./data-repo/sample1.tsv ./single/sampletest.tsv
variant-filter ./data-repo/sample1.tsv ./single/sampletest.tsv TTT
gtf-analyze ./single/samplegtf.gtf
variant-seq ./single/sample1.tsv ./single/sample.fasta
download-genome yes
acmg-transcript ./single/sample1.tsv
sequence-profile ./single/sample1.tsv ./data-repo/sample.fasta 10 10
population-variant-search newversion-population G samplename
coordinate-search newversion-population 14464 16495 samplename
annotation-search newversion-population AL645608.6 samplename
pathogenicity-filter newversion-population 0.0 1.5 samplename
population-variant-searcholder oldversion-population G samplename
coordinate-searcholder oldversion-population 14464 16495 samplename
annotation-searcholder oldversion-population WASH7P samplename
pathogenicity-filterolder oldversion-population 0 1.5 samplename
transcript-search newversion-population ENST00000635509.2 samplename
alt-allele newversion-population T samplename
alt-allele-older oldversion-population T samplename
alt-ref-allele newversion-population A T samplename
alt-ref-allele-older oldversion-population A T samplename
- Acknowledgements: Funded through Development of a universal fast-response platform, based on RNA technology,ensuring the national drug and epidemiological safety. 2021/ABM/05/00004-00
- Project PI and Informal queries: Prof. Luiza Handschuh: [email protected].
- eVaiultities code related queries: Dr. Gaurav Sablok: [email protected].
Gaurav Sablok
Instytut Chemii Bioorganicznej
Polskiej Akademii Nauk
ul. Noskowskiego 12/14 | 61-704, Poznań
Poland