Open DavisCammann opened 1 year ago
Is the LiftOver function of SumStatsRehab only intended to be from lower genome builds to hg38?
Yes. It was originally designed for lift over of earlier builds to build 38. We did not really consider using it in the opposite direction.
Hello, I have been having an issue converting a GWAS file from genome build 38 to genome build 37 (hg19). In order to do this, I specified hg38 for "build" in the .json file of the GWAS, and then provided the two prepared DBSNP files from hg19 (--dbsnp-1 and --dbsnp-2), as well as the --chain-file that specifies conversion from hg38 to hg19.
This results in the program finishing at Step 3 without performing LiftOver as below:
To see if it would do anything, I decided to instead specify the "build" of my hg38 GWAS to hg19 in the .json file, and provide the same --dbsnp and --chain-file files as above, which resulted in LiftOver being performed successfully:
This produces a file which appears to be successfully transferred from hg38 to hg19. Is the LiftOver function of SumStatsRehab only intended to be from lower genome builds to hg38? It seems like specifying an hg38 GWAS as hg19, and then matching the dbsnp files to that lower build with a chain file that goes from hg38 to hg19 works. However, specifying the hg38 GWAS as its actual build does nothing if you want to convert it to build hg19.