Skip to content

Latest commit

 

History

History
53 lines (39 loc) · 1.42 KB

README.md

File metadata and controls

53 lines (39 loc) · 1.42 KB

#Calling mutations from MA lines

##Required libs

Needs to be compiled/on path:

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