Output Files
(BASE is a placeholder for the text passed to the --basename option.)
| File | Description |
|---|---|
| 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. |