QTL lead variants

These are the standard QTLtools (https://qtltools.github.io/qtltools/) output files with the following column names:

1. The phenotype group ID (here a gene ID)
2. The chromosome ID of the phenotype group
3. The start position of the phenotype group
4. The end position of the phenotype group
5. The strand orientation of the phenotype group
6. The top phenotype in the group (here an exon ID)
7. The total number of phenotypes in the group (i.e. #exons)
8. The total number of variants tested in cis
9. The distance between the phenotype group and the tested variant (accounting for strand orientation)
10. The ID of the top variant
11. The chromosome ID of the top variant
12. The start position of the top variant
13. The end position of the top variant
14. The number of degrees of freedom used to compute the P-values
15. Dummy
16. The first parameter value of the fitted beta distribution
17. The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region)
18. The nominal P-value of association between the top phenotype and the top variant in cis
19. The corresponding regression slope
20. The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the direct method (i.e. empirircal P-value)
21. The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis

I prefer to use the following short column names

1. group_id
2. pheno_chr
3. pheno_start
4. pheno_end
5. strand
6. phenotype_id
7. group_size
8. n_cis_snps
9. distance
10. snp_id
11. snp_chr
12. snp_start
13. snp_end
14. df
15. dummy
16. beta1
17. beta2
18. p_nominal
19. slope
20. p_perm
21. p_beta