I am looking for a given mutation in IGV, which accepts coordinates in the form of
chr<X>:<Y>
Where X is the chromosome number and Y is the base location in that chromosome.
Eg. chr6:26091179
which has the following attributes:
Gene: HFE|LOC108783645
Marker: rs1799945
Position: chr6:26091179
Additionally, an interval can be written like
chr<X>:<Y>-<Z>
So basically from base located at Y to Z.
My questions are:
1) How do I convert HFE|LOC108783645
to chr6:26091179
(and vice-versa)?
2) How do I convert rs1799945
to chr6:26091179
(and vice-versa)?
3) On a different example, how do I convert something like codon 109 of exon 3 of beta globin gene (GTG->TTG)
to chr<X>:<Y>
(or chr<X>:<Y>-<Z>
)?
Why are there so many ways to specify positions in genes? For me the most clear way is chr<X>:<Y>
, all the others leave me guessing...
chr:pos
notations are independent of reference sequence versions.chr6:26091179
in GRCh38 is not the same in GRCh37. $\endgroup$