All-FIT - Allele-Frequency-based Imputation of Tumor Purity infers specimen purity from tumor-only samples sequenced with deep sequencing. It is developed in Khiabanian Lab by Jui Wan Loh and Hossein Khiabanian.
All-FIT is implemented in Python 3.
How to run
The following Python package is required:
Just clone this repository and run All-FIT as described below.
Running All-FIT on test/input/sampleFile1.txt with columns containing uniqueID, variant allele frequencies, depth and ploidy information:
python All-FIT.py -i All-FIT/test/input/sampleFile1.txt -d All-FIT/test/output -o sampleFile1 sampleFile1 0.78 0.77,0.78,0.79
Inferred purity is printed on stardard output as shown above (estimated purity = 0.78 with two standard deviation ranges from 0.77 to 0.79); one text file and two png files are generated in All-FIT/test/output.
python All-FIT.py --help
for detailed description of input parameters