associate a variant with a mutation in hg19

Question

[bioguy24]

I am looking for a tool or script that will associate or identify a variant coordinate in hg19 to a mutation.

The below is an example that shows a variant from a vcf associated with a "c." mutation, but I am not sure how this was done.

 2  166895930   166895930   -   T   intronic    SCN1A   c.2589+19_2589+20insA;c.2589+19delA
 5  88100640    88100640    -   A   intronic    MEF2C   c.55-21_55-20insT
 5  125929001   125929002   AC  -   intronic    ALDH7A1 c.246+41_246+42delGT
 5  125929004   125929004   C   -   intronic    ALDH7A1 c.246+39delG

I use annovar and that seems to identify the majority, but not all. Previously we would get the above output using a vcf and I am trying to figure out how it was done. Thank you :).

Answer 1

[Petr Ponomarenko]

This "mutation" c. info is called HGVS codes http://varnomen.hgvs.org/ . Maybe you were using an older version of HGVS (based on the style of HGVS codes) http://www.hgvs.org/mutnomen/ Since you were doing it some time ago, I assume you using VEP http://www.ensembl.org/info/docs/tools/vep/index.html It has command line tool. (or maybe you used SNPeff http://snpeff.sourceforge.net/) We have our own solution for this https://agx.alapy.com/ in beta testing. It does lots of other things, but it is not a command line tool, so will be harder for integration, but we can create one for your needs (you can send request to at [e-mail]). Technicaly you need good reference assembly, good transcripts, good alignment that takes care of mismatches properly and is careful about splice sites, then you use HGVS standard to change mutation to proper one (see guidlines) and then encode it according to HGVS