pjvandehaar
commented
4 months ago Thanks for pointing out “glob” vs “glob-files”! I just fixed it.
For rsids, I think you’re right. Anyways, it’s a harmless change, right? If you make a PR with that change I’ll merge it. Or did you already make one? I can’t remember anymore. Actually, I think it would be even better to just match on chr:pos and ignore ref/alt.
On Wed, Feb 14, 2024 at 9:34 PM Jie Huang @.***> wrote:
Hi, there:
I noticed pheweb phenolist glob-files on this instruction page https://github.com/statgen/pheweb/blob/master/etc/detailed-loading-instructions.md#configuration-options. However, it won't work. It should be just "glob", not "glob-files".
The first time when I run pheweb process, I think pheweb automatically download the huge dbsnp reference files. If I already have these huge dbsnp files downloaded for another software, how could I speficy its location in the config.py file so that it won't need to be re-downloaded?
Previously, I have pointed out that many GWAS simply report A1/A2, not the strict REF/ALT. Once the reference genomes get bigger and bigger, the REF/ALT specification would become really indefinite and inconsistent. Therefore, I strongly suggest that pheweb would accommodate the use of A1/A2 and be able to map rsIDs with a better flexibility. Otherwise, most SNPs in a GWAS would have no mapped rsIDs after running pheweb. You guys only need to change one line (line 140), for add_rsids.py. Before： rsids = [rsid['rsid'] for rsid in rsid_group if cpra['ref'] == rsid['ref'] and are_match(cpra['alt'], rsid['alt'])] After： rsids = [rsid['rsid'] for rsid in rsid_group if (cpra['ref'] == rsid['ref'] and are_match(cpra['alt'], rsid['alt'])) or (cpra['ref'] == rsid['alt'] and are_match(cpra['alt'], rsid['ref']))]
Please kindly consider this.
Thank you & best regards, Jie
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jielab
Hi, there:
I noticed pheweb phenolist glob-files on this instruction page https://github.com/statgen/pheweb/blob/master/etc/detailed-loading-instructions.md#configuration-options. However, it won't work. It should be just "glob", not "glob-files".
The first time when I run pheweb process, I think pheweb automatically download the huge dbsnp reference files. If I already have these huge dbsnp files downloaded for another software, how could I speficy its location in the config.py file so that it won't need to be re-downloaded?
Previously, I have pointed out that many GWAS simply report A1/A2, not the strict REF/ALT. Once the reference genomes get bigger and bigger, the REF/ALT specification would become really indefinite and inconsistent. Therefore, I strongly suggest that pheweb would accommodate the use of A1/A2 and be able to map rsIDs with a better flexibility. Otherwise, most SNPs in a GWAS would have no mapped rsIDs after running pheweb. You guys only need to change one line (line 140), for add_rsids.py. Before：
rsids = [rsid['rsid'] for rsid in rsid_group if cpra['ref'] == rsid['ref'] and are_match(cpra['alt'], rsid['alt'])]After：rsids = [rsid['rsid'] for rsid in rsid_group if (cpra['ref'] == rsid['ref'] and are_match(cpra['alt'], rsid['alt'])) or (cpra['ref'] == rsid['alt'] and are_match(cpra['alt'], rsid['ref']))]Please kindly consider this.
Thank you & best regards, Jie