/replace_allele_counts

This repo helps to replace the allele counts in maf file after genotyping

Primary LanguagePythonApache License 2.0Apache-2.0

replace_allele_counts

This repo helps to replace the allele counts in maf file after genotyping

Requirements:

Build Status codecov

replace_allele_counts.py

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.