This repo helps to replace the allele counts in maf file after genotyping
Based on Mutation Annotation Format (MAF)
- Takes in a MAF with FillOut based on GetBaseCountsMultiSample and outputs a MAF (Note: You will loose the comments if any present in the MAF file)
python replace_allele_counts.py --help
usage: replace_allele_counts.py [options]
This tool helps to replace the allele counts from the caller with the allele
counts of GetBaseCountMultiSample
optional arguments:
-h, --help show this help message and exit
-v, --verbose make lots of noise
-imaf SomeID.maf, --input-maf SomeID.maf
Input maf file which needs to be fixed
-ifill SomeID.fillout.txt, --fillout SomeID.fillout.txt
Input fillout file created by GetBaseCountMultiSample
using the input maf
-omaf SomeID.maf, --output-maf SomeID.maf
Output maf file name
-o /somepath/output, --outDir /somepath/output
Full Path to the output dir.