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