frequency-scanner

Reports frequency of all possible permutations of single nucleotide changes for a group of fastq files. Counts every minor variant below a certain frequency of each fastq as mapped against a provided fasta file.

Dependencies

This program requires that you have the following programs installed and working on your path

1. Python
2. fastq_quality_filter[http://hannonlab.cshl.edu/fastx_toolkit/]
3. bwa-mem[http://bio-bwa.sourceforge.net/] (reccomend installing through a package manager)
4. samtools[http://samtools.sourceforge.net/] (reccomend installing through a package manager)
5. bam-readcount[https://github.com/genome/bam-readcount] You have to build this one yourself. I reccomend downloading directly into the folder you're installing this program into. Then make and build right in this folder.

Running

Once you've got the above dependencies working and on your path just run frequency_scanner.py with the only argument being your reference fasta file. It'll run on all the fastq files in your folder. You can get a list of configurable options by typing python frequency_scanenr.py -h

The output will be a big csv with all the frequencies in it. This can be easily imported into R and you can make pretty pictures.