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daiqile96 / OTTERS

A powerful TWAS framework leveraging summary-level reference data
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geno_dir #5

Closed LeTing-Chow closed 11 months ago

LeTing-Chow commented 1 year ago

Thanks for providing a powerful tool! Could you tell me how to download the VCF files used in geno_dir? I used the 1000genome files(http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/), but it didn't work I got this: AttributeError: 'NoneType' object has no attribute 'size' Traceback: File "/home/g854597751/OTTERS/training.py", line 287, in thread_process target_dir, target_sst, median_N = prep.prepare(target=target, File "/home/g854597751/OTTERS/prepare.py", line 64, in prepare if not snp_overlap.size:

Thank you very much!

daiqile96 commented 11 months ago

Hi, OTTERS requires PLINK binary files for the genotypes. See examples Exp_geno.bim, Exp_geno.fam, Exp_geno.bed under here.

Some codes for converting VCF files to PLINK binary files can be found here.