Genomic Position Converter (OLD) 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

Warning: This is an older version and is no longer updated. We encourage you to use the new, updated version with new utilities and improvements, particularly the ability to convert Hs1 genome positions (T2T-CHM13 telomere-to-telomere human genome sequence). Go to NEW Version

Chrom: Pos hg19            Pos hg38          (* 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.