Functional annotation generation¶
The generation of functional annotation matrix relies on two types of information (files)
- The functional annotation bed files
- The chromosome and position information of each SNP from GWAS summary data file
If using PAINTOR script to generate functional annotation matrix¶
Header | Option | Note |
---|---|---|
chr | required | |
pos | required |
Note
- Make sure that the functional annotation bed file are sorted, because the AnnotateLocus.py script used a specific algorithm and unsorted functional annotation bed file will lead to wrong function annotation matrix.
- Make sure that the chromosome nomenclature is the same in the GWAS file and the functional annotation bed file. e.g. both should be chr1 or both should be 1
Example code¶
Note
This should not be used directly since it applies to specific files
python AnnotateLocus.py
--input annotation_paths_list
--locus gwas_summary_3_4750808.processed
--out gwas_summary_3_4750808.processed.annotations
--chr chr
--pos pos
If using bedtools to generate functional annotation matrix¶
to be added