Hi I am trying to do mr using Gwas summary data. However, only P and EAF and harmonisation codes were given. I can calculate c score by p, but couldn't know the sign of Z. Could I refer the orientation of z score by harmonisation codes. Table of harmonisation codes Code Description of process 1
Palindromic; Infer strand; Forward strand; Alleles correct
2
Palindromic; Infer strand; Forward strand; Flipped alleles
3
Palindromic; Infer strand; Reverse strand; Alleles correct
4
Palindromic; Infer strand; Reverse strand; Flipped alleles
5
Palindromic; Assume forward strand; Alleles correct
6
Palindromic; Assume forward strand; Flipped alleles
7
Palindromic; Assume reverse strand; Alleles correct
8
Palindromic; Assume reverse strand; Flipped alleles
9
Palindromic; Drop palindromic; Not orientated
10
Forward strand; Alleles correct
11
Forward strand; Flipped alleles
12
Reverse strand; Alleles correct
13
Reverse strand; Flipped alleles
14
Required fields are not known; Not orientated
15
No matching variants in reference VCF; Not orientated
16
Multiple matching variants in reference VCF; Not orientated
17
Palindromic; Infer strand; EAF or reference VCF AF not known; Not orientated
18
Palindromic; Infer strand; EAF < specified minor allele frequency threshold; Not orientated
Headers will be coerced to the 'harmonised format'.
Addition harmonised data columns will be added.
Rows may be removed.
Variant ID, chromosome and base pair location may change (likely).
