infer the orientation of z score by using the harmonisation codes
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11 weeks ago
celia • 0

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).

Gwas MR • 141 views
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