Software running¶
As abovementioned, after preprocessing, running fine-mapping software is usually straightforward and you are recommended to look through each software's documentation
PAINTOR¶
Example code¶
paintor -input input_loci_list
-in input_dir
-out output_dir
-Zhead Zscore
-LDname ld
-enumerate 1
-annotations annotation1,annotation2,annotation3
fgwas¶
Note
fgwas does NOT allow SNPs to have the same position and it will raise an error. Make sure SNPs have unique position before using fgwas
Example code¶
fgwas -i input_file
-fine
-print
-w annotation1+annotation2
-o outputfile