Genomic Position Converter
hg19 to hg38 and vice versa
Release 2020_09, by Ivano Zara
For any problem write to ivano.zara.bio@gmail.com
This program derives the correspondences between the different genomic releases,
using the 'hg19ToHg38.over.chain and hg38ToHg19.over.chain' file of the UCSC,
where the alignment data of the different genomic sequences are reported


Genomic position converter
The conversion is performed only if a valid alignment is found on the same chromosome
Chrom:
 

(* see note) Also consider mismatches <= as correctly aligned
Warning, some particular cases

Discordant data is sometimes obtained from the genomic alignment files (hgxxtoHgxx.over.chain).
Here are some examples. By clicking on them you can see the discrepancies.

from hg19 Chr1:1582862      from Hg19, two different positions point to the same position in hg38
from hg19 Chr1:325635      there is a conversion from hg19 to hg38 but not the reverse
from hg19 Chr1:325139      there is a conversion from hg19 to hg38 but not the reverse
(* note) The 'OverChain' file (by UCSC) of genomic alignments does not consider small mismatches to be aligned.
Therefore positions that fall into these mismatches would not be converted.
This APP also allows you to convert genomic positions that fall into mismatched regions whose maximum length can be set by the user.
A warning is displayed if the position falls within a region of mismatches.