MSeqDR mvTool Documentation

mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation
 

MSeqDR mtDNA Tool set (mvTool) is a one-stop mtDNA variant annotation and analysis Web service. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php

Background:

mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (http://www.mitomap.org) and HmtDB (http://www.hmtdb.uniba.it/hmdb).  mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates ab initio mtDNA variants.

Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mito-genomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar. mvTools also provides mtDNA somatic variants annotations. ‘mvTool API’ is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures.  The results are reported as hyperlinked html tables, JSON, Excel and VCF formats.

Mitochondrial DNA variant nomenclature has multiple existing systems used in literature and in different institutes. The major ways are:

1. Classical I: used in literature, PhyloTree, Haplogrep, 8527, 8993G, 8993d, 5787_5789d, 1494.1T, 7472.XA
2. Classical II: T8993G
3. HGVS Committee: NC_012920.1:m.8993T>G, reference version is required. This is the recommended format, being required by journals and NCBI/ClinVar. The short naming like m.8993T>G is also widely used in literature, assuming rCRS as reference.
4. VCF-style input: Tab-delimited, with at least the first 5 columns in vcf format
5. Ensembl: MT:g.8993T>G
6. Mutalyzer: NC_012920.1:g.8993T>G
7. Potential non-standard: 8527A>G

mvTool supports the chromosome names as any of the following:
chrM, chM, chrMT, chMT, M, MT, NC_012920.1.

The mvTool universal variant converter can convert the various combinations of these formats into a standard variant list in the rCRS-based HGVS (1-3) formats.

The current mtDNA variant data is mostly based on the default revised Cambridge sequence (rCRS, accession number NC_012920.1). The use of YRI (Yoruban, accession number NC_001807.4, derived from AF347015) as the mitochondrial reference genome is discouraged by NCBI. Since some commercial SNP array platforms used or may still use YRI as the reference genome, mvTool can convert YRI-based positions into rCRS-based positions, but only for backward compatibility. The mvTool does not covert rCRS coordinates to YRI-based coordinates.

Running mvTool:

mvTool functions in two modes, “Web” and “API.” In Web mode, the user can paste a list of mtDNA variants into the Web form and have annotations returned as either an HTML table or as a downloadable Excel file. The input form is prepopulated with example variants in mixed formats to enable quick start, and includes help documentation describing the technical details shown when the tool is first opened. Upon submission, each job is sent to a 24‐CPU dedicated server with 32 GB of RAM and 4 TB of HDD. With this set‐up, most analyses of one mtDNA genome (usually comprised of less than 100 variants) take under 1 min to complete.

In the API mode, users can use the UNIX curl command to remotely upload a file in VCF, HGVS, or classical mtDNA variant formats to retrieve annotation back as either JSON or annotated VCF files. There are three ways to access MSeqDR mvTool API, using syntax similar to the following example commands:

  1. VCF input, new VCF returned with MSeqDR annotations appended to INFO column:   curl ‐s ‐X POST https://mseqdr.org/mtannotapi.php?format=cpmvcf –data‐binary  @demo00001.MT.vcf ‐o demo00001.MT.annot.vcf
  2. VCF input, JSON return, with full annotation details:   curl ‐s ‐X POST https://mseqdr.org/mtannotapi.php?format=vcf  –data‐binary  @demo00001.MT.vcf ‐o demo00001.MT.vcf.json
  3. HGVS or classical mtDNA variant input formats, JSON return, with full annotations:   curl ‐s ‐X POST https://mseqdr.org/mtannotapi.php?format=hgvs –data‐binary  @mvtool_hgvs.txt ‐o mvtool_hgvs.txt.json

*Disclaimer: This mvTool and associated data are strictly for research purpose only, they are not clinically-validated nor applicable for clinical diagnosis.

 
mvTool change log:
 
2018-10-17
mvTool is updated with data from Mitomap 2018 Update #3 (September 1, 2018) which added 125 new variants from 598 new full-length (FL) and 445 control region (CR) GenBank sequences. This brings the Mitomap total of non-disease variants to 13,656, the number of FL sequences to 46,092.
 
2018-03-27
 
2018-02-07
 
 2017-09-25

Tool update: MSeqDR mvTool Version 2.0: mtDNA variant annotation and analysis web-service with API.

Input mtDNA variants in any of the 7 major formats, mixed formats input is supported. The results are returned as multiple html tables, as well as a downloadable combined Excel file. An API is implemented, which takes inputs in VCF, HGVS, or classical mtDNA variant nomenclatures, and returns annotated vcf or json outputs.

 
2016-06-18
mvToo V1.0 was presented during the MSeqDR/Genesis Tutorial Workshop at UMDF Mitochondrial Medicine 2016.
 

MSeqDR mvTool collaborators and data sources:

 

Contact:

mvTool Development:  Dr. Lishuang Shen (lshen86@gmail.com) , or use the online feedback.

MSeqDR Consortium Leaders:  Dr. Marni Falk ( falkm@email.chop.edu), Dr. Xiaowu Gai  (XGai@chla.usc.edu)

 

Dr. Lishuang SHEN

Lishuang Shen MSeqDR WebMaster, Sr. Bioinformatics Scientist, Center for Personalized Medicine, Children's Hospital of Los Angeles, Email: lishen@chla.usc.edu, shen_lishuang@yahoo.com, Suite 300, 2100 W 3rd St, Los Angeles, CA 90057

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