## CNA-seq / Define CNA-seq experiment

### Description

This tool takes as input a number of BAM files, produces binned read counts for each sample, combines the results into a single table, and generates the phenodata table required for further analyses.

### Parameters

- Experiment type (genome=hg19, binSize=1kbp, type=SR50; genome=hg19, binSize=5kbp, type=SR50; genome=hg19, binSize=10kbp, type=SR50; genome=hg19, binSize=15kbp, type=SR50; genome=hg19, binSize=30kbp, type=SR50; genome=hg19, binSize=50kbp, type=SR50; genome=hg19, binSize=100kbp, type=SR50; genome=hg19, binSize=500kbp, type=SR50; genome=hg19, binSize=1000kbp, type=SR50) [genome=hg19, binSize=15kbp, type=SR50]
- Is first mate read (yes, no, any) [any]
- Is second mate read (yes, no, any) [any]
- Is not primary read (yes, no, any) [any]
- Is not passing quality controls (yes, no, any) [no]
- Is duplicate (yes, no, any) [no]
- Minimum mapping quality (0..n) [37]

### Details

Takes as input a number of BAM files, divides the specified genome build into bins of the specified size, and counts the number of reads in each bin. The implemented package is QDNAseq.

### Output

Data table with read counts per sample and accompanying phenodata table.

### References

QDNAseq:
Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res In Press.