Quick start

To perform the simplest fine-mapping using easyfinemap, including determining independent loci using the distance-based method and calculating the posterior probability for each SNP using the abf method, you can follow these steps:

1. Download the example data (ignore if already downloaded):

   git clone https://github.com/Jianhua-Wang/easyfinemap.git
   cd easyfinemap/exampledata
   

2. Determine independent loci using the distance-based method:

   $ easyfinemap get-loci -m  distance PH251.sig.txt.gz PH251.distance
   

3. Calculate the posterior probability for each SNP using the abf method:

   $ easyfinemap fine-mapping \
       -m abf \
       --credible-threshold 0.95 \
       PH251.txt.gz \
       PH251.distance.loci.txt \
       PH251.distance.leadsnp.txt \
       PH251.abf.txt
   

For more advanced features and parameter explanations, please refer to the documentation。