deepseqcoverageqc 0.3.3

Compute coverage QC metrics for deep targeted sequencing data

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

Contact

• Dr. Pandurang Kolekar
• Dr. Xiaotu Ma

COPYRIGHT

Copyright © 2023 Pandurang Kolekar, St. Jude Children's Research Hospital