Can I liftover hs37d5 to hg38 using hg19ToHg38 chain file?

Question

[ConvolutedGenome]

Hello,

I am currently working on analyzing the somatic mutation data from the PCAWG project. In the main PCAWG paper (https://www.nature.com/articles/s41586-020-1969-6), they mentioned aligning their whole-genome sequencing (WGS) reads to the hs37d5 reference genome.

Based on this information, I want to convert the .maf file that I downloaded from PCAWG to the hg38 reference genome. My approach involves converting the .maf file to .bed format and using UCSC liftOver to perform the conversion to hg38. (before converting it back to .maf @_@)

However, I'm facing an issue as I cannot locate the chain file required for this conversion. I have checked the UCSC downloads page (https://hgdownload.soe.ucsc.edu/downloads.html) but there are none for hs37d5.

My question is: Can I use the hg19ToHg38 chain file (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz) for this conversion? Am I making a HUGE mistake here?

Thank you in advance!!!

Answer 1

[Zhenyu Zhang]

"d" here stands for decoy sequences. They are extra short unmapped contigs. These doesn't change the major contigs, and doesn't affect liftover.

[ConvolutedGenome]

Sooo, its essentially the same as hg19 then?

Meaning I can use hg19To38 Chain file to convert hs37d5 to hg38?

[Zhenyu Zhang]

yes, you can just use the regular chain file