MR_instruments_selection

Strategy:

1. best SNP from pvalue in locus breaker region overlapping cis region and passing bonferroni threshold

   • input: locusbreaker results + sumstats
   • parameters/other imputs: Bonferroni threshold, cis trans mapping file
   • steps:
     • cis/trans map the locus breaker results
     • filter the cis
     • compute the f stats for the best snps from LB results
     • if F stats >=10, select the best snps
     • if not:
       1. extract the locusbreaker region from summary statistics
       2. select only the snp passing Bonferroni threshold
       3. compute fstats and filter out those with Fstats <=10
       4. select the most significant snp if any remaining
   • output: list of instruments (<=1 per target)

2. insturments from conditional using conditional beta and SE estimates

   • input: conditional sumstats
   • parameters/other inputs: cis trans mapping file
   • steps:
     • mapping: output is sumstats with additionaval cis trans variable
     • filtering cis
       (Alternative strategy: take end and start (of cis region defined by TSS) from mapping file and extract the cis region)\
     • calculate fstats from conditional beta and SE
     • filter out fstats <=10
     • save remaining snps (with beta and SE pvalue)

3. insturments from conditional using unconditional beta and SE estimates

   • input: instruments defined on conditional sumstats, unconditional sumstats
   • parameters/other imputs:
   • steps
     • keep only the snps in the previous list of instruments
     • save remaining snps (with beta and SE pvalue)