Human Genomic Position Converter from / to gemome release:    GRCh37/hg19   ;   GRCh38 / hg38   ;   T2T-CHM13 v2.0 / hs1 Release 2024_04, by Ivano Zara For any problem write to ivano.zara.bio@gmail.com

this program uses LiftOver files (over.chain) downloaded from the UCSC website to convert positions between different genomic releases. In particular, use the files: hg19ToHg38.over.chain, hg38ToHg19.over.chain, hg38ToHs1.over.chain, hs1ToHg38.over.chain , hs1ToHg19.over.chain where the alignment data of the different genomic sequences are reported This application, for daily use, is more intuitive and simple than other similar applications New: Implemented the program with the new T2T-CHM13 / hs1 genomic release (telomere-to-telomere human genome sequence). It is now possible to convert the genomic positions between hg19, hg38 and hs1.

Genomic position converter The conversion is performed only if a valid alignment is found on the same chromosome View our example : from hg38/GRCh38 Chr17:1 pos:41771799 (Gene JUP)

New conversion Chrom: Input Genomic position Genomic release from hg19 (GRCh37)    from hg38 (GRCh38 )    from hs1 (T2T-CHM13)

(* see note) I consider the alignment as correct even if the genomic position falls within a mismatch are less than or equal to nt

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. If you want to see an example, click here from hg38 Chr1:1654188 Note2: These program only uses the alignment of the same chromosome. Does not return conversions with different chromosomes. Example hg38 chr1: 494198 towards hs1 (use hg38ToHs1.over.chain) there is no correspondence in the same chromosome: the program does not return a conversion, while instead there is an alignment in hs1 with chr5:181888219 (see UCSC).