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.