129. 2015 Nov BroadE workshop handson tutorial materials

IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here

created by Geraldine_VdAuwera

on 2015-11-16

We are scheduled to do 2 hands-on modules at the BroadE GATK workshop at the Broad Institute this Thursday, Nov. 19.

The tutorial materials for each module include the following:

• Workshop dataset and an appendix document containing detailed instructions for preparing for the workshop
• Tutorial worksheet containing the actual exercises done in the workshop

Attendees will receive a printout of the worksheets for the module to which they have registered. We will not provide printouts of the appendix documents.

If you are registered to attend, you must have downloaded the materials and followed the instructions before the workshop starts, otherwise you will not be able to follow along and your workshop experience will be unsatisfying. We certainly don't want that to happen, so be sure to do your homework as follows below the fold. Be sure to identify correctly which workshop you are registered for!

Variant Discovery (morning session)

Get the dataset + appendix bundle: 5 minutes

Note that the file and directory names make reference to ASHG 2015 because these materials were originally developed for the GATK workshop we taught at the ASHG 2015 meeting. There, that's one mystery cleared up!

• Download the 52 Mb zip file to the laptop you will bring to the workshop, and save it where you want the tutorial files to sit.
• Open the zip file; this will create a directory called ASGH15_GATK.
• Open the ASGH15_GATK directory, look at the contents and read the extremely brief README.txt file.

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

• Open the PDF document called ASGH15_GATK-Appendix.
• Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the ASGH15_GATK-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

• Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
• Download all 3 software packages (GATK, Samtools, IGV) to the laptop you will bring to the workshop.
• Copy the program files of all three to the ASGH15_GATK directory.
• Run the test commands for GATK and Samtools, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV.

Callset Filtering & Evaluation (afternoon session)

The appendix file is now available from this link. The data bundle is available here.

Be sure to have done the workshop preparation homework as outlined below and described in the Appendix!

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

• Open the PDF document called BroadE2015-Filtering_Tutorial-Appendix (linked above).
• Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the BroadE2015-Filtering_Tutorial-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

• Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
• Download all software packages listed (GATK, RStudio, IGV) to the laptop you will bring to the workshop.
• Create a directory called BroadE2015 where you will put tutorial files.
• Copy the program files of all three to the BroadE2015 directory.
• Run the test commands for GATK and RStudio/ggplot, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV and RStudio.

Updated on 2015-11-19

From Jon on 2015-11-17

Must I use Java 7 / JRE 1.7? My machine is running java 1.8.0_45.

From Geraldine_VdAuwera on 2015-11-17

We have not yet tested GATK on java 1.8 so we don’t know what problems might occur. I would suggest you at least download java 1.7 to have it available so that if you do run into difficulties due to java version you can rapidly switch to that.

From Jon on 2015-11-19

Hi Geraldine – are the test files for variant filtering available?

From Sheila on 2015-11-19

Hi Jon,

They will be uploaded soon. It’s not a big bundle, so you can all download it during during the talk if necessary

-Sheila

From Geraldine_VdAuwera on 2015-11-19

I posted the data bundle here: https://drive.google.com/file/d/0BwTg3aXzGxEDeTVBNEUzUE9OS1U/view?usp=sharing