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Tutorial:Apply ALoFT to identify loss-of-function somatic or germline variants
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17 months ago
Shicheng Guo ♦ 7.5k

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
  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:

  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
ALoFT Tutorial • 139 views

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