CNA-seq / Define CNA-seq experiment

Description

This tool takes as input a number of files with binned read counts, combines them 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

Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions. Manuscript submitted.