Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
gravatar for Shicheng Guo
5 days ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

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
  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

Here is for LOF extract from pre-calculated hg19 annotation.

for(i in 1:22){
newdata<-subset(data,data[,13]<0.05 & data[,15] !="Tolerant")[,c(1,2,9,15)]
perl -p -i -e 's/chr//i' aloft.hg19.txt
perl -p -i -e 's/Dominant/Dom/i' aloft.hg19.txt
perl -p -i -e 's/Recessive/Rec/i' aloft.hg19.txt
gzip aloft.hg19.txt

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 • 64 views
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