Converting genomic coordinates to cDNA coordinates

[Margaret Hoang]

Hi,  I have the following information for mutations in GRCh37/hg19:

1. Transcript Accession

2. Gene Accession

3. Genomic Coordinate and Base sequence (i.e. g.chr1:2000-2000C>T)

I’d like to express this as cDNA coordinates including the transcriptional base (i.e. c.190G>A).

Do you have suggestions on how to do this?

Thank you,

Margaret

~~~
Margaret Hoang, Ph.D.

Postdoctoral Fellow
Ludwig Center for Cancer Genetics and Therapeutics
The Sidney Kimmel Comprehensive Cancer Center
Johns Hopkins University, School of Medicine
1650 Orleans St., CRB1 Room 520, Baltimore, MD 21231
Office:  410-955-8878
Fax:  410-955-0548
Email:  mlho...@gmail.com

[Jonathan Casper]

Hello Margaret,

Thank you for your question about converting genomic variants into other formats. One of our engineers suggests that the following tool may provide almost exactly what you need: https://mutalyzer.nl/positionConverter. You would need to make some minor changes: the "g." should appear after the colon (e.g., g.chr1:2000-2000C>T --> chr1:g.2000-2000C>T).

You may also be interested in our Variant Annotation Integrator (VAI) at http://genome.ucsc.edu/cgi-bin/hgVai. With a list of variants in pgSNP or VCF format, the VAI can provide coordinates for the variants in cDNA and CDS for a variety of gene/transcript sets along with consequent changes to the transcriptional base(s).

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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