Can seqminer reads and merges these large GWAS files?

[jielab]

Hi, there:

A recent Nature Genetics paper posted 35 large GWAS files at https://doi.org/10.35092/yhjc.12355382. Compared with the regular .tsv format, I assume that these BED format files should be much faster to be queries and managed.

Now I want to combine the BETA and SE of all these 35 GWAS into a single file. Reading each of them into R using read.table() and then merge() would take impossible computational time and that did not utilize the BED format. Can you please let me know if seqminer or something else could do this merging?

Similarly, these GWAS files don’t have rsIDs, and I need to add them. Can you please also suggest a good approach to do this. If these were VCF files, I could use bcftools annotate to add rsID from a dbSNP reference file.

Thank you & Best regards,
Jie