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

if you use the new application (launched from the same 'human genomics' section)
you can convert the positions not only of the hg19 and hg38 genomes,
but also of hs1 (T2T-CHM13 genomic release, telomere-to-telomere human genome sequence).
Furthermore, improvements have been made in alignment
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
View Alignment Table chromosome 1 (from hg19ToHg38.over.chain by UCSC)
>
Warning
Pos hg19 Pos hg38
325635    - - ->    493702
0    <- - -    493702
from hg19 to hg38 and vice versa, the positions are not concordant
Around genomic sequences
(any different bases are in red) 
                                         325635
hg19 TCATGACTGTGAGGCCATTTCCAGGCCTAGTGCCT G CCTCGTGGCTGACTCTTGAAGCCCAAAACTTCCTC
hg38 GAGGAAGTTTTGGGCTTCAAGAGTCAGCCACGAGG C AGGCACTAGGCCTGGAAATGGCCTCACAGTCATGA
                                         493702
(* 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.