Output files

VisCap_run_info.xls
Provides a complete summary of the VisCap analysis

session.Rdata
Stores the R workspace for each VisCap run

QC_cnv_heatmap.pdf
Compares normalized, fractional coverage of each exon across all samples

QC_cnv_boxplot.pdf
Displays the distribution of log2 ratios for each sample by box-and-whisker plots

QC_cnv_boxplot.xls
Provides the summary metrics and pass/fail status for each sample in the batch based on the analysis of all genes in the region of interest

QC_chrX_pre-scale.pdf
Shows the average coverage of all data points on the X chromosome for males and females in the batch before any scale or compensation for males only having one X. All males will look deleted as compared to females.

QC_chrX_pre-scale.xls
Provides the pre-scale summary metrics and pass/fail status for each sample based on the analysis of X chromosome genes in the region of interest

QC_chrX_post-scale.pdf
Shows the average coverage of all data points on the X chromosome for males and females in the batch after any scale or compensation for males only having one X. Males and females should behave similarly.

QC_chrX_post-scale.xls
Provides the post-scale summary metrics and pass/fail status for each sample based on the analysis of X chromosome genes in the region of interest

sexes.xls
Provides computationally predicted patient genders based on pre-scale X plots

cnv_boxplot_outliers.xls
Contains all calls for all intervals across all samples [losses=-1, copy-neutral=0, gains=1]

log2_ratio_table.xls
Contains all log2 ratios for all intervals across all samples in the batch

.cleaned.plot.pdf [one file per sample]
Displays the log2 ratios across all intervals overlaid with the threshold lines used for copy number variation detection

.cleaned.cnvs.xls [one file per sample]
Provides the metrics, genomic coordinates, and gene/exon identity for each copy number variation detected