Birdsuite is a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus.

References:

• Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll, Alec Wysoker, James Nemesh, Simon Cawley, Earl Hubbell, Jim Veitch, Patrick J Collins, Katayoon Darvishi, Charles Lee, Marcia M Nizzari, Stacey B Gabriel, Shaun Purcell, Mark J Daly & David Altshuler
  Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
  Nature Genetics V. 40, N.10 (2008), p.1253-1260;

• Birdsuite Home page

• Module Name: birdsuite (see the modules page for more information)
• Unusual environment variables set
  • BS_HOME  installation directory
  • BS_BIN       executable directory
  • BS_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=16g --cpus-per-task=16
[user@cn3335 ~]$module load birdsuite
[+] Loading singularity  4.0.1  on cn4172
[+] Loading birdsuite  20231107

[user@biowulf]$ Birdsuite 
Version File not found.  Version checking disabled.
Argument is required: genderFile
Argument is required: basename
Error: No cel files specified.

usage: Birdsuite [options] cel-files...

Run the whole birdsuite pipeline.
Steps are:
1: apt_probeset_summarize
2: annotate_allele_summaries
3: cn_locus_summarize
4: cn_probeset_summarize
5: canary
6: cn_create_exclude_list
7: birdseed
8: pre_birdseye
9: birdseye
10: post_birdseye
11: larry_bird
12: birdsuite_report

defaultBlockSize              Default block size Default: 0

firstStep                     What step to start with in birdsuite process.
                              Default: 1

platform                      Which platform the birdsuite data comes from.
                              Options:[AffyMetrix,Illumina] Default: AffyMetrix

genomeBuild                   What version of locus metadata to use.  Must be
                              one of: ['hg17', 'hg18']. Default: hg18

configFile                    Birdsuite config file.  Stores sets of command
                              line arguments. Any argument provided in the
                              argument file is overridden by a command line
                              argument.

canary.priors                 CNV priors file, can be population specific.

noLsf                         Do not use LSF to run birdseye jobs.  Run them
                              synchronously instead. Default: false

metadataDir                   Location of metadata files. Default:
                              /humgen/affy_info/GAPProduction/dev

noOp                          Outputs all the commands birdsuite would use to
                              run all sub programs, but programs are not run.
                              Useful to debug. If this command is used, also
                              use --noLsf. Default: false

defaultMemUsage               Default memory used in Megs Default: 4000

genderFile                    File containing a line for each sample in the
                              data file. 0=female, 1=male, 2=unknown. This file
                              must have a header line 'gender'.

canary.allele_freq_weight     Allele frequency model weight.  Change with
                              caution!

apt_probeset_summarize.force  Passed through to apt-probeset-summarize.
                              Default: false

lsfQueue                      Use given LSF queue for parallelizing birdseye.
                              Default: birdseed

chipType                      Which chip type the cel files are. This is used
                              to select the appropriate metadata files.
                              Default: GenomeWideSNP_6

noversionCheck                Do not check for latest version Default: false

outputDir                     Where to write the large volume of output data.
                              When running on LSF, this should probably be in
                              /local/scratch, so long as there is a way to
                              retrieve the files when done. Default: .

lastStep                      What step to end with in birdsuite process.
                              Default: 12

exeDir                        Location of executable files. Default:
                              /fg/software/Affymetrix/GAPProduction/dev

basename                      Used to name all the output files.

celFiles                      Text file specifying cel files to process, one
                              per line the first line being 'cel_files'.
                              Default: get cel files from command line.

[user@cn3335 ~]$ ls $BS_BIN
annotate_allele_summaries  birdseedqc   birdsuite_report        cn_locus_summarize  pre_birdseye
apt_probeset_summarize     birdseye_64  canary                  larry_bird          shell
birdseed                   Birdsuite    cn_create_exclude_list  post_birdseye
[user@cn3335 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$