huang-j / tarpan

Tracking edits during rotation in 2020

TarPan Viewer is a tool used to visually inspect targeted panel sequencing data.

You can access the demo site here (it may take a moment to load example data).

Built With

• R
• R Shiny
• Python

Dependencies

The easiest and fastest way to run TarPan is to install R Studio.

Python 3.x + Pandas

Installation of TarPan Viewer

1. Clone the repository

git clone https://github.com/tcashby/tarpan.git

2. Create a new R Studio project in the cloned directory and open ui.r, server.r, and install.r.

3. Install dependencies (this command should work, but you may need to manually intervene)

source("install.R")

4. Assuming the dependencies installed correctly, you should now be able to run the application in R Studio.

Limitations

Due to limitations of SQLite, databases can not be created on NSF/SMB mounted volumes.

Scripts

In order to utilize the Python scripts, Python must be installed.

Python can be installed standalone or through Anaconda.

Python Setup

1. Download Python 3.7.x from: https://www.python.org/downloads/
2. Install Python (If Windows, select "Add PATH" on install)
3. Install Pandas via Command Prompt or Shell prompt.

  python -m pip install Pandas

If issues occur, this Python tutorial might help.

Script Arguments

Argument	Description
-refgen	Reference Genome
-pipeline	Pipeline Name
-targetbed	Target Bed File
-groupbed	Group Bed File
-blacklist	Blacklist Bed File
-bedfile	Other Bed File
-bedtype	Other Bed File Type
-sampid	Sample ID
-normid	Normal ID
-mutfile	Mutation File
-muttool	Mutation File Tool
-svfile	Structural Variant File
-svtool	Structural Variant File Tool
-snp	SNP File
-met	Metrics File
-depth	Depth File
-log	Log File
-sex	Patient Sex
-patid	Patient Identifier

DB Create

required_args = -db, -refgen, -targetbed, -groupbed

create_db.py -db "Tarpan.db" -refgen "hg19" -pipeline "pipeline01"
             -targetbed "target.bed" -groupbed "group.bed" -blacklist "blacklist.bed"
             -bedfile "other.bed" -bedtype "other"

DB Update

required_args = -db

update_db.py -db "Tarpan.db" -refgen "hg19" -pipeline "pipeline01"
             -targetbed "target.bed" -groupbed "group.bed" -blacklist "blacklist.bed"
             -bedfile "other.bed" -bedtype "other"

Entry Create

required_args = -db, -sampid

create_db_entry.py -db "Tarpan.db" -sampid "sample01" -normid "sample01Norm"
                   -mutfile "sample01Mut.vcf" -muttool "Strelka2"
                   -mutfile "sample01Mut02.vcf" -muttool "MuTect"
                   -svfile "sample01SV.vcf" -svtool "Manta"
                   -snp "sample01SNP.csv" -met "sample01MET.csv" -depth "sample01DEP.csv"
                   -log "sample01.log" -patid "patientId" -sex "Male"

Entry Update

required_args = -db, -sampid

update_db_entry.py -db "Tarpan.db" -sampid "sample01" -normid "sample01Norm"
                   -mutfile "sample01Mut.vcf" -muttool "Strelka2"
                   -svfile "sample01SV.vcf" -svtool "Manta"
                   -snp "sample01SNP.csv" -met "sample01MET.csv" -depth "sample01DEP.csv"
                   -log "sample01.log" -patid "patientId" -sex "Male"

Entry Delete

required_args = -db, -sampid

delete_db_entry.py -db "Tarpan.db" -sampid "sample01"