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 :).