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All-FIT

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

Dependencies

The following Python package is required:

Installation

Just clone this repository and run All-FIT as described below.

Usage example

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.

Try:

python All-FIT.py  --help

for detailed description of input parameters

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All-FIT - Allele-Frequency-based Imputation of Tumor Purity

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