#Calling mutations from MA lines

##Required libs

Needs to be compiled/on path:

• bamtools
• eigen
• Boost::program_options

Provided in this repo

• bamtools headers (for bamtools-utils, not in the normal include headers)

##Compilation

At present cmake handles a basic build. Presuming bamtools and eigein are on your path you can do this

cmake .
make
./accuMUlate -c test/test_params.ini -b test/test.bam -r test/test.fasta -o test/test.out
./pp -c test/pp_params.ini -b test/test.bam -i test/test.out 

The last line will run the caller on a test dateset with 6 000 bases, and show find mutations in each gene.

##TODO

• have the main loop run the analysis from

  • BAM file
  • kist of sample IDs (one ancestor, rest descendants)
  • Model Params: *theta *mu *nfreqs *phi-haploid *phi-diploid
  • [BED file of coords to include]
  • [probability threshold]
  • [quality cut-off]

• Boost PO/YAML/some other format to handle run variables

• Manage build across platforms w/ CMake

• Optimize model code

• Clean up sample mapping/base calling

• Post-processor for putative mutations

• Create .vcf and annotations files from snps

• Make real test suite