APOCO

APOE reads Counter

Introduction

The program counts the number of reads pertaining to specific APOE alleles from BAM files in a given folder.

Please note that the program won't be able to find APOE e1 alleles in case the read lengths do not span both the RSID positions (GRCh38: chr19:44908684 and chr19:44908822), which means a read length of at least 138bp.

Installation

Go to the releases section and downlod the binary file for your system.

Usage

The default threads are counted based on the system. The number shown as default here pertains to the system this program was built on.

Usage of apoco:
  -chr
        Use this flag if the reference chromosomes are named with "chr" in the names (e.g. chr1, chr2, chrX, etc.)
  -f string
        Folder containing BAM files
  -hg int
        Human genome version (19 or 38) (default 38)
  -max int
        Maximum read length (default 150)
  -min int
        Minimum read length (default 100)
  -o string
        Output file name (default "./apoeCounts.tsv")
  -qual int
        Minimum mapping quality (default 30)
  -t int
        Number of threads to use (default 32)

Results

Unless specified an output file location, the program outputs a tab delimited apoeCounts.tsv file with the sample name and raw read counts for each APOE allele in the current directory.

Example:

Sample	APOE1	APOE2	APOE3	APOE4
TestA	0	2	9498	78
TestB	0	0	6284	4875