DeepSeqCoverageQC
Compute coverage QC metrics for deep targeted sequencing data
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Quick Start
Using Docker
docker run -it pskolekar/deepseqcoverageqc:0.3.3 DeepSeqCoverageQC --help
Using Miniconda
conda create --name DeepSeqCoverageQC python==3.9
conda activate DeepSeqCoverageQC
python -m pip install deepseqcoverageqc
DeepSeqCoverageQC --help
Using Pip
Note Requires Python version >=3.9
pip install deepseqcoverageqc
Usage
Please refer to the detailed documentation here
DeepSeqCoverageQC is a command line interface (CLI) app with the following commands
$ DeepSeqCoverageQC --help
Usage: DeepSeqCoverageQC [OPTIONS] COMMAND [ARGS]...
Compute coverageQC for targeted deep sequencing data
╭─ Options ─────────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ buildIndex Generate index for the panel │
│ computeCoverageQC Compute coverageQC metrics across panel regions. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Build panel index
$ DeepSeqCoverageQC buildIndex --help
Generate index for the panel
╭─ Options ─────────────────────────────────────────────────────────────────────────╮
│ * --panelFile PATH File with panel regions. File should have four │
│ tab-delimited columns: Chr, Start, End, Gene │
│ [required] │
│ --outfile PATH Output file name. │
│ --padding INTEGER Padding (bp) for regions. │
│ --chr/--no-chr Add 'chr' prefix │
│ --help Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Compute region and sample level QC metrics
$ DeepSeqCoverageQC computeCoverageQC --help
Usage: DeepSeqCoverageQC computeCoverageQC [OPTIONS]
Compute coverageQC metrics across panel regions.
╭─ Options ─────────────────────────────────────────────────────────────────────────╮
│ * --panelPosFile PATH File with panel positions as generated │
│ by buildIndex command.File should have │
│ six columns: Chr.Pos, Chr, Start, End, │
│ Gene, RegionLength │
│ [required] │
│ * --summaryPosFile PATH File with unique positions in the panel │
│ to compute sample level summary │
│ statistics. File should have one column: │
│ Chr.Pos, as generated by buildIndex │
│ command. │
│ [required] │
│ * --countFile PATH Count file(s) generated by SequencErr │
│ program. File(s) should've seven │
│ columns: Chr, Pos, A_Q_30, C_Q_30, │
│ G_Q_30, T_Q_30, N_Q_30 │
│ [required] │
│ --outdir PATH Output directory path. │
│ --outSummary/--no-outSummary Output counts at summary positions │
│ --help Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Publication
Manuscript under preparation
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COPYRIGHT
Copyright © 2023 Pandurang Kolekar, St. Jude Children's Research Hospital
1 maintainer
Metadata
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Release files for deepseqcoverageqc 0.3.3
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