Output Files

(BASE is a placeholder for the text passed to the --basename option.)

FileDescription
apt-probeset-summarize.log This file is produced by apt_probeset_summarize, the first step in Birdsuite.
BASE.allele_summary Allele summary file produced by apt_probeset_summarize.
BASE.annotated_summary Allele summary file with probe locus information for each probe(set), sorted in genomic order.
BASE.locus_summary Same as annotated_summary above, except values for A and B alleles for a SNP are averaged together.
BASE.probeset_summary A single intensity value for each common-CNP,sample pair.
BASE.canary_calls Calls file for common CNPs, with a copy number for each common-CNP,sample pair.
BASE.canary_confs Confidence file that is the partner to canary_calls file, indicated the confidence of each Canary call. 0=most confident, 1=least confident.
BASE.canary_log Log produced by Canary.
BASE.birdseed_exclusions For each probe(set), a list of the 0-based sample indices for samples that have unusual copy number as determined by Canary.
BASE.birdseed_calls Conventional Birdseed genotype call file. 0=AA, 1=AB, 2=BB, -1=no call
BASE.birdseed_confs Confidence file that is partner to birdseed_calls file. 0=most confident, 1=least confident.
BASE.birdseed_clusters SNP clusters found in the process of running Birdseed.
BASE.*.birdseye_dir 24 subdirectories, each with data so that Birdseye can be run in parallel on each chromosome.
BASE.birdseye_canary_calls Merged Birdseye and Canary calls. Each line contains a copy number count for a chromosome and range, and a confidence. In this file, a larger number indicates higher confidence.
BASE.birdseye_calls Raw Birdseye calls. This is just the concatenation of the Birdseye calls from each birdseye_dir subdirectory.
BASE.birdseye_cn_clusters CN probe clusters used by Birdseye.
BASE.larry_bird_calls SNP genotype calls with arbitrary copy number. Each call is of the form N,M , where N is the number of the A allele and M is the number of the B allele. No-call is represented as -1,-1.
BASE.larry_bird_confs Confidence file that is the partner to larry_bird_calls. 0=most confident, 1=least confident.
BASE.report.txt Summary statistics of Larry Bird SNP calls in the spirit of those produced by apt_probeset_genotype. The various CNx_percent columns are the percentage of SNPs for that sample for which the number of copies (i.e. N+M for a call N,M) equals x. These columns sum to 100. The diallelic percentages (AB_percent, AA_percent, BB_percent) have as their denominator the number of diallelic calls, so these three percentages sum to 100.
SAMPLE.birdsuite.rpt The same information as found in BASE.report.txt, split by cel file.