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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Quick way to extend LD calculation to other reference panels #42

Open pwh124 opened 5 years ago

pwh124 commented 5 years ago

Hello,

The script for running LD calculations is very specific for 1000G haplotype data. However, recently published reports (PMID: 28942963) show that using small external reference panels for summary statistics from large GWAS can negatively affect fine-mapping results.

Would there be a quick way to adapt the LD script for a different reference panel (like HRC)? From my naive reading of the script, it seems like just eliminating filtering on pop_ids might do the trick.

Paul

uod12345 commented 3 years ago

Hi Paul, does the trick work? I have the same issue since my SNPs are imputed using HRC and not 1000G.