Utility Programs

ProgramDescription
birdsuite_qc.py

birdsuite_qc.py is a convenience program that runs mini-DM and calls the gender the cel files. It produces a list of cel files that pass the mini-DM threshold, and also a gender file for those cel files. These two files can then be input to birdsuite.sh using the --celFiles and --genderFile options.

Usage:
EXEDIR/birdsuite_qc.py --cel_files_out output.cels --gender_out output.gender --metadata_dir METADATADIR --exe_dir EXEDIR cel-files...

You may wish to edit birdsuite_qc.py so that your EXEDIR and METADATADIR are the default values.

birdsuite_pipeline.py birdsuite_pipeline.py is a convenience program that runs birdsuite_qc.py on a list of cel files, producing a list of files that pass mini-DM threshold along with their genders, and then launches birdsuite.sh on those cel files.
make_bed.py make_bed.py produces a BED (binary PED) file in the format expected by PLINK from Birdseed or Larry Bird calls and confidences files. See PLINK documentation for details on BED files. By using make_bed.py to create a BED file, make_bim.py (see below) to create a BIM file, and creating a FAM file yourself from your pedigree data, you will have the basic inputs needed to run PLINK.
make_bim.py make_bim.py produces a BIM (binary MAP) file in the format expected by PLINK. In order to use make_bim.py, you will need to download from the Affymetrix website the SNP annotation file for the chip you are using and the genome build you desire. See PLINK documentation for details on BIM files.