Convert chromosomal position to gene sequence position

[Stephanbio]

I have a list of mutations with their chromosomal locations like
chr1:6266188-6266188
chr22:5443534-5443534 .....

I know how to fetch a list of genes with ucsc browser and/or galaxy that intersects with my mutations. and their accompanying DNA sequence

But in order to know wich nucleotide in the gene sequence is mutated I have to know the position in the gene.
Is there a way to convert the chromosomal position to nucleotide position in a gene. so that I can easy invistigate what kind of mutation it is.
dream result would be:
gene1 blabla lenght: 1...789 your mutation is in place 88
or actaXacta
or actaNacta

[ZhengXia]

If you fetch gene region from annotation database such as UCSC knowngene.txt, you can easily do it.

I have a list of mutations with their chromosomal locations like
chr1:6266188-6266188
chr22:5443534-5443534 .....

I know how to fetch a list of genes with ucsc browser and/or galaxy that intersects with my mutations. and their accompanying DNA sequence

But in order to know wich nucleotide in the gene sequence is mutated I have to know the position in the gene.
Is there a way to convert the chromosomal position to nucleotide position in a gene. so that I can easy invistigate what kind of mutation it is.
dream result would be:
gene1 blabla lenght: 1...789 your mutation is in place 88
or actaXacta
or actaNacta

[Stephanbio]

Now that's exactly my question! If it's so easy, can you explain further

[Jonathan]

http://seqanswers.com/wiki/ANNOVAR

is what your are looking for.

[Joann]

more open research

I suggest ANNOVAR for publication in the new journal Open Research Computation--recently introduced elsewhere on this site.

[Stephanbio]

Thanx , I think ANNOVAR is exactly what i need
I'm playing with it right now.