Footprints_v1

Footprints runs a c based tool, foots, that uses samtools to count the number of bases in your bam file with a minimum coverage of your choice.

Welcome to footprints

Thank you for downloading footprints v.0.1.

Footprints counts the number of bases in your bam file with a minimum coverage of your choice.

The sequencing footprint of your bam can then be used to accurately calculate mutation burden.

We recommend you select a minimum coverage value -n that reflects the minimum number of reads your pipeline requires to call variants.

Installation

To install please make sure you have the following requirements

Requirements

1. samtools-0.1.19
2. bedtools

If you don't have this version of samtools installed please follow steps below to install and add to path. Otherwise skip to the next step.

Install Samtools v.0.1.19

You make require --no-check-certificates here. If you are not comfortable with using this link please find an alternative download online.

$ wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2

$ tar -xf samtools-0.1.19.tar.bz2

$ cd samtools-0.1.19

$ make

$ export PATH=/path/to/samtools-0.1.19:$PATH

Install Footprints v.0.1

$ ./configure
$ make

Run Footprints v.0.1

$ ./footprints -h

Program: Footprint calculation (for accurately calculating sequencing footprint)

Version: 0.1

Usage: ./footprints -b <bam> -i <intervals bed file> -n <minimum coverage(default=5)> -o <output file>

Options:
        -b      Bam: Bam file or directory containing bam files on which footprints are to be calculated [required]
        -i      Intervals bed file: Genomic intervals on which to operate [required]
        -n      Minimum coverage: Minimum number of reads a base needs to be covered by to count as part of callable footprint [default=5]
        -o      Output file: Text output for results [default=STDOUT]
        -h      Help: Does what it says on the tin

Input

Any input bams must be indexed.

You can input one bam file: -b /path/to/sample1.bam

Or a directory containing multiple bams: -b /path/to/dir

Output

By default, each bamfiles footprint is written to standard out: Calculating footprint on file: sample1.bam Minimum coverage selected: 5 Number of base pairs in file with greater than 5 coverage: 4910521 Or you can output the results into a tab seperated file of your choice. You can select this option by adding -o output.txt

BAM	BP
sample1.bam	4910521
sample2.bam	4906269
sample3.bam	4930272