HapMuC is a somatic mutation caller, which can utilize the information of heterozygous germline variants near candidate mutations. It takes a tumor bam and a normal bam as inputs, and generates a list of candidate somatic mutations.

Please make sure developer tools for the OS are available (usually installable in batch, but should include make, gcc/g++ etc.) The version we tested is GCC 4.8.1.

For convenience, the prerequisites of HapMuC are all included in this repository (You can find them at libs/). The prerequisites are:

• Boost 1.45.0 (modified to include only the subset of the library used by HapMuC)
• SAMtools 0.1.19
  • SAMtools has two dependencies (vid. Samtools - Primer):
    • GNU curses library
    • ZLib compression library
• BEDTools 2.17.0
  • BEDTools also depends on ZLib (vid. BEDTools FAQ)

To prepare them, please execute the following script in your shell:

% make dependencies

Just execute the following script in your shell:

% make

Ruby and Python are required to run associated scripts for making candidate windows. The versions we tested were listed below:

• Ruby 1.9.3
• Python 2.7.3.

Also, the Python script requires the fisher module for calculating the p-values of Fisher's exact test.

HapMuC workflow is consisting from three steps. Let's try it on the sample bam files, which we prepared in the tests folder. Please go to tests/data/1.

../../../libs/samtools-0.1.19/samtools mpileup -B -f ../random_ref.fasta normal.bam > normal.pileup
../../../libs/samtools-0.1.19/samtools mpileup -B -f ../random_ref.fasta tumor.bam > tumor.pileup

sh ../../../utils/make_windows.sh tumor.pileup normal.pileup ./

Outputs:

• ./cand_somatic
  • Candidate somatic mutations, which passed the minimum criteria. (NOTE: you can set the parameters in utils/search_variants.rb )
• ./cand_hetero_germline
  • Heterozygous germline variants. Also, you can check the criteria in utils/search_variants.rb.
• ./windows
  • A list of candidate windows, which is generated based on the above two files using bedtools window.

../../../bin/hapmuc -a tumor.bam -b normal.bam -f ../random_ref.fasta -w windows -o result/mc

You can check the results in results/mc.calls.txt

A dataset and scripts for simulation are available here: https://github.com/usuyama/hapmuc_simulation .

Submitted.

Copyright © 2013 Naoto Usuyama
Released under the GNU General Public License, Version 3.0.

This implementation forked from the program Dindel, which is licensed under the GPLv3.