Allele frequency counter with BAM file and VCF file
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README.md

README.md

README for SnpExp

Introduction

SnpExp is an allele frequency counter with BAM file and VCF file.

Install

Before building this project, you have to install libbam provided by Li et al. (http://samtools.sourceforge.net/). If you build SAMtools bam.h, bgzf.h and libbam.o files will appear in the directory. These files should be copied to paths for header files and library files typically at /usr/local/include/ and /usr/local/lib/.

If these files are correctly installed, you can setup and build the program.

./configure
make

Built binaries can be installed your executable paths.

Usage of SnpExp

snpexp [-h] [--version] 
       <options> bam1 bam2 ...

##Options ###-V FILENAME Filename of variants provided in VCF format

###-o FILENAME Filename of output. If no filename is given, the result will be outputted to standard output.

###-G FILENAME GTF file of gene annotation which includes genic positions.

###-I Retain intergenic SNPs.

###-verbose Verbose mode.

###-s strain1,strain2 Straind such as C57BL6NJ, 129S1 for mice

###-m number (default 0) Minimum number of detected bases. If all bam files do not include the given number of bases, the SNPs will not be outputted.

bam files

BAM files should be sorted before processing. They should also share the same set of chromosomes because the program analyze data chromosome by chromosome.

-h

Show command help.