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").

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

library(devtools)
install_github("wtsi-hgi/seq_autoqc", subdir="bamcheckr")

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:

Rscript bamcheck_augment_summary.R --help

Usage with defaults is as simple as:

Rscript bamcheck_augment_summary.R input.bamcheck output.bamcheck

These defaults are equivalent to:

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