Here, I open a tutorial to show the my usage experience of ALoFT to identify loss-of-function somatic or germline variants.

1) Install ALoFT: same as all other python software very hard to install.

2) Download ALoFT from ALoFT website

3) Python 2.7.5 (default, Oct 30 2018, 23:45:53) will be a little easy to install it quickly.

  cd /home/local/MFLDCLIN/guosa/hpc/tools
  wget http://org.gersteinlab.aloft.s3-website-us-east-1.amazonaws.com/aloft-1.0.zip
  unzip aloft-1.0.zip
  wget http://org.gersteinlab.aloft.s3-website-us-east-1.amazonaws.com/data.zip
  unzip data.zip
  PATH=/home/local/MFLDCLIN/guosa/hpc/tools/aloft/aloft-annotate:$PATH
  source ~/.bashrc

With the above command, you install ALoFT and download annotation database and add it to .bashrc. Now let's start to use it.

aloft --vcf All_samples_Exome_QC.DG.vcf --output All_samples_Exome_QC.DG --data /home/local/MFLDCLIN/guosa/hpc/tools/aloft/aloft-annotate/data.txt

Feedback:

Question: How long time it is required for aloft to annotate 2,650,576 variants? 
Answer: 20min-60min depends on the performance of your PC

The potential problem you might meet and how to solve it:

1. Majority problem will be caused by the Python version and python code setting. Try different Python version.
2. If you meet tab and space problem, try: autopep8 -i aloft