WES Report
Stephen Kelly
July 31, 2017
1 Overview
Project ID:
demo-output
Results ID:
results1
| sample | |
|---|---|
| 1 | Sample1 |
| 2 | Sample10 |
| 3 | Sample11 |
| 4 | Sample12 |
| 5 | Sample13 |
| 6 | Sample14 |
| 7 | Sample15 |
| 8 | Sample16 |
| 9 | Sample17 |
| 10 | Sample18 |
| 11 | Sample19 |
| 12 | Sample2 |
| 13 | Sample20 |
| 14 | Sample21 |
| 15 | Sample22 |
| 16 | Sample23 |
| 17 | Sample24 |
| 18 | Sample3 |
| 19 | Sample4 |
| 20 | Sample5 |
| 21 | Sample6 |
| 22 | Sample7 |
| 23 | Sample8 |
| 24 | Sample9 |
1.1 Mapping
1.2 Coverage Per Sample
1.2.1 Mean
1.2.2 Per Cutoff
2 Target Regions
2.1 Coverage Per Region
2.2 Regions With Low Coverage (<50)
2.3 Regions with 0 Coverage
3 Variant Calling
3.1 Haplotype Calling
3.1.1 GATK
3.1.1.1 Number of Mutations
3.1.1.1.1 Plot
3.1.1.1.2 Table
3.1.1.2 Quality Scores
3.1.2 Lo Freq
3.1.2.1 Number of Mutations
3.1.2.1.1 Plot
3.1.2.1.2 Table
3.1.2.2 Quality Scores
4 System Information
## System:
## phoenix2
## Linux 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016## System user:
## kellys04## System location:
## /ifs/home/kellys04/projects/Clinical_580_gene_panel/molecpathlab/NGS580_WES-development/demo-output/results1/sns-wes-downstream-analysis## Git Remote:
## origin https://github.com/NYU-Molecular-Pathology/sns-wes-downstream-analysis.git (fetch)
## Git Remote:
## origin https://github.com/NYU-Molecular-Pathology/sns-wes-downstream-analysis.git (push)## Git branch and commit
## master: d8864cf9289e3ced19a9bba67fc9f87b7a56f5cb## Time and Date of report creation:
## Mon Jul 31 13:51:38 EDT 2017## R version 3.3.0 (2016-05-03)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS release 6.8 (Final)
##
## locale:
## [1] C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets base
##
## other attached packages:
## [1] DT_0.2 data.table_1.10.4 reshape2_1.4.2 ggplot2_2.2.1
## [5] knitr_1.16
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.12 magrittr_1.5 munsell_0.4.3 colorspace_1.3-2
## [5] rlang_0.1.1 highr_0.6 stringr_1.2.0 plyr_1.8.4
## [9] tools_3.3.0 grid_3.3.0 gtable_0.2.0 htmltools_0.3.6
## [13] yaml_2.1.14 lazyeval_0.2.0 rprojroot_1.2 digest_0.6.12
## [17] tibble_1.3.3 htmlwidgets_0.9 evaluate_0.10.1 rmarkdown_1.6
## [21] labeling_0.3 stringi_1.1.5 methods_3.3.0 scales_0.4.1
## [25] backports_1.1.0 jsonlite_1.5