https://github.com/wtsi-hgi/seq_autoqc
Additional high-throughput sequencing autoQC steps
https://github.com/wtsi-hgi/seq_autoqc
Last synced: about 2 months ago
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Additional high-throughput sequencing autoQC steps
- Host: GitHub
- URL: https://github.com/wtsi-hgi/seq_autoqc
- Owner: wtsi-hgi
- Created: 2013-01-16T13:29:00.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2015-11-10T16:38:40.000Z (over 9 years ago)
- Last Synced: 2025-01-26T18:48:27.868Z (3 months ago)
- Language: R
- Size: 265 KB
- Stars: 1
- Watchers: 18
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
seq_autoqc
==========
These routines run on data produced by bamcheck and are used as part of the autoqc process in HGI pipelines.
bamcheck files used to be produced by the `bamcheck` program but are now incorporated into `samtools` and produced by the `samtools stats` command (as of the 1.0 release candidates beginning with "0.2.0-rc1").
bamcheckr
---------
An R package for reading and writing bamcheck data, and for calculating indel_peaks,
quality_dropoff, and base_content_deviation.
This package can be installed directly from git using `devtools`
```R
library(devtools)
install_github("wtsi-hgi/seq_autoqc", subdir="bamcheckr")
```
bamcheck_augment_summary.R
--------------------------
An R script that takes bamcheck as input and produces augmented bamcheck as output, in which
additional Summary Number (SN) entries are added for indel peaks, quality dropoff, and base
content deviation.
You can obtain help by running:
```bash
Rscript bamcheck_augment_summary.R --help
```
Usage with defaults is as simple as:
```bash
Rscript bamcheck_augment_summary.R input.bamcheck output.bamcheck
```
These defaults are equivalent to:
```bash
Rscript bamcheck_augment_summary.R --indel-runmed-k=25 --indel-baseline-method=runmed --base-content-runmed-k=25 --base-content-baseline-method=mean --quality-dropoff-runmed-k=25 --quality-dropoff-ignore-edge-cycles=3 --quality-dropoff-high-iqr-threshold=1 input.bamcheck output.bamcheck
```