b37 liftover

Question

[spesks]

Hi! I have vcf files that were get with b37 reference, and I need to liftover them to hg38 (and then to t2t if it's possible). The problem is that there are no chain files that converts b37 to hg19 or b37 to hg38. What is the righ way of solving the problem? Should i rename the chromosomes according to hg19 ?

[GenoMax]

There is no difference in the main chromosomes between b37 and hg19 (except Chr Y and MT, see table below) .

https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies

Unless you are doing something very specific, it may be reasonable to use hg19 files.

[spesks]

Thank you! renaming chrs according to hg19 and using hg19 chain files helped.

Answer 1

[Giulio Genovese]

Using BCFtools/liftover will automatically take care of:

• flexible contig names (e.g. 18 vs. chr18) in the chain file (you still have use the correct fasta files)
• not changing the coordinates of variants on the mitochondrial genome if it detects that target and query mitochondrial sequences have the same length (you can use chain file hg19ToHg38.over.chain.gz with b37, even if b37 and hg19 have different mitochrondrial sequences ... coordinates for mitochondrial variants will be left unchanged)