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alleleCount on Biowulf and helix
Calculates genotype frequencies of a SNPMatrix. This component tests each SNP for its Hardy-Weinberg equilibrium. If there are NA values, the frequencies of missing value per sample in the input file are calculated.

alleleCount Environment Module

WARNING

Based on the distribution as received, the module is named "alleleCount"
while the principal program is named "alleleCounter".

Before running the alleleCounter program, you must add the alleleCount environment module.into your shell environment. This is most easily done by using the module commands, as in the example below:

[user@biowulf]$
[user@biowulf]$ module avail alleleCount               (see what versions are available)
----- /usr/local/lmod/modulefiles ------
   alleleCount/1.2.1
[user@biowulf]$
[user@biowulf]$ module load alleleCount                       (load the default version and required packages)
[user@biowulf]$
[user@biowulf]$ module list                            (see what versions are loaded)
Currently Loaded Modules:
  1) alleleCount/1.2.1
[user@biowulf]$
[user@biowulf]$ module unload alleleCount                  (unload bamsurgeon and required packages)
[user@biowulf]$


Running the alleleCounter program

[user@biowulf]$
[user@biowulf]$ bin/alleleCounter --help
Usage: alleleCounter -l loci_file.txt -b sample.bam -o output.txt [-m int] [-r ref.fa.fai]

 -l  --loci-file [file]           Path to loci file.
 -b  --hts-file [file]            Path to sample HTS file.
 -o  --output-file [file]         Path write output file.

Optional
 -r  --ref-file [file]           Path to reference fasta index file.
                                 NB. If cram format is supplied via -b and the reference listed in the cram header can't be found alleleCounter may fail to work correctly.
 -m  --min-base-qual [int]       Minimum base quality [Default: 20].
 -q  --min-map-qual [int]        Minimum mapping quality [Default: 35].
 -v  --version                   Display version number.
 -h  --help                      Display this usage information.
[user@biowulf]$


alleleCount Utility Programs

With the alleleCount module environment loaded, the following utility programs are provided:

To see the command usage, use the shell command:

In some cases, you can get a little more information with the shell command


Documentation