NYU-Molecular-Pathology/oncomine_automation

oncomine automation

User Guide to Oncomine Automation

Workflow from run initiation to review of annotated variants

• Annotate variants from the oncomine annotator
• Focus on variants of interest
• Visualize and interpret variants
• Link variants to relevant clinical evidence

Software required:

1. python3

Python is a high-level, interpreted, general-purpose programming language. It is used to execute automated tasks and conduct data analysis.

2. watchdog

Python API library and shell utilities to monitor file system events.

3. ion_automation

An in-house automated workflow to generate quality control plots/reports and select variants from Oncomine Focus and Myeloid Assay NGS sequencing data.

Workflow Diagram

Directory Structure

• oncomine solid

|— amplicon.dropout.dropoff 
|— downloads
|- dropoff
|- reports

• myeloidseq

|— amplicon.dropout.dropoff 
|— downloads
|- worksheet.dropoffs
|- reports

Step by step guide to generate MyeloSeq automated report

1. create a new folder in the /Molecular/IonTorrent/myeloseqer_test/amplicon.dropout.dropoff folder for the run.
2. copy basecall QC matrix files from /MOLECULAR LAB ONLY/NYU-MyeloSeqer/Patient data to amplicon.dropout.dropoff
3. get a copy of the myeloseq worksheet for the run from the MOLECULAR LAB ONLY/NYU-MyeloSeqer/Worksheets-Wetlab folder
4. drop the worksheet to the worksheet.dropoffs subfolder under the IonTorrent folder on the Molecular shared drive

Note: The workflow automatically starts in a few seconds. It takes up to 10~30 minutes to generate QC plots/reports, to select confident calls, and to save filtered variants in a csv and excel format

5. copy CSV and dropout reports to the /MOLECULAR LAB ONLY/NYU-MyeloSeqer/Patient data

Step by step guide to generate Oncomine Solid automated report

1. copy basecall QC matrix files from /MOLECULAR LAB ONLY/NYU-MyeloSeqer/Patient data to /Molecular/IonTorrent/oncosolid_autoreport/amplicon.dropout.dropoff
2. get a copy of the myeloseq worksheet for the run from the MOLECULAR LAB ONLY/Oncomine Patient Data/Worksheets-Wetlab folder
3. drop the worksheet of the run to the worksheet subfolder under the IonTorrent folder on the Molecular shared drive

Note: The workflow automatically starts in a few seconds. It takes up to 10~20 minutes to generate QC plots/reports, to select confident calls, and to save filtered variants in a csv and excel format

4. copy CSV and dropout reports to the /MOLECULAR LAB ONLY/Oncomine Patient Data/Patient data

Step by step guide to generate report manually

1. Oncomine Solid

1. ssh to bigpurple with your Kerberos ID
2. log into the ionreporter server as an admin user
3. go to the ion_report directory
4. complete steps 1 ~ 3 in the auto report section
5. execute ion_runner.py

ssh ionadmin@ionreporter.nyumc.org
cd /home/ionadmin/ion_report
python3 ion_runner.py /mnt/Z_drive/Molecular/IonTorrent/oncosolid_autoreport/worksheet/22-MGON9.xlsm

2. MyeloSeq

1. ssh to bigpurple with your Kerberos ID
2. log into the ionreporter server as an admin user
3. go to the myeloseq_report directory
4. complete steps 1 ~ 3 in the auto report section
5. execute myelo_runner.py

ssh ionadmin@ionreporter.nyumc.org
cd /home/ionadmin/myeloseq_report
python3 myelo_runner.py /mnt/Z_drive/Molecular/IonTorrent/myeloseqer_test/worksheet.dropoffs/22-MGMQ24.xlsm

Maintaining automated workflow

1. ion_report workflow

1. ssh to bigpurple with your Kerberos ID
2. log into the ionreporter server as an admin user
3. change to the ion_report directory
4. start or stop the ion_watchdog daemon process

ssh ionadmin@ionreporter.nyumc.org
cd /home/ionadmin/myeloseq_report
sh ion_watchdog.sh start [stop]

2. myelo_report workflow

1. ssh to bigpurple with your Kerberos ID
2. log into the ionreporter server as an admin user
3. change to the myeloseq_report directory
4. start or stop the myelo_watchdog daemon process

ssh ionadmin@ionreporter.nyumc.org
cd /home/ionadmin/myeloseq_report
sh myelo_watchdog.sh start [stop]