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Support #23

Test the DRAGEN GATK best practice workflow on a WGS GiaB sample

Added by Gerrit Botha about 7 years ago. Updated almost 7 years ago.

Status:
Resolved
Priority:
Normal
Assignee:
Jon Ambler
Start date:
03/13/2018
Due date:
% Done:

100%

Estimated time:

Description

We need to test this workflow.

The sample data for the child of a GiaB trio NA12878 has been shared with Jon. The WGS sequencing has been done on a Illumina HiSeq 2000 at X50. 100bp paired end.

  • The forward reads can be downloaded here
  • The reverse reads can be downloaded here

There is a local copy of the reads at CHPC as well, but the permissions to where it is stored just need to be opened.

Once we have done testing we might need to see if we can also get hold of a publicly available HiSeq X Ten sample (150bp) just to see how much need to be adjusted for the alignment step.

History

#1

Updated by Gerrit Botha about 7 years ago

  • Description updated (diff)
#2

Updated by Gerrit Botha about 7 years ago

Hi Jon,

Just want to check how it is going with this and if you need any help?

Regards,
Gerrit

#3

Updated by Jon Ambler about 7 years ago

Hi Gerrit,

I'm just waiting on the CPGR to give me a time to come in so they can show me the system.

#4

Updated by Gerrit Botha about 7 years ago

Ok

#5

Updated by Gerrit Botha about 7 years ago

We had a BST meeting. Seems like there is a slight diversion from the original plan and suggestions made. Maybe better just to follow BST meetings to understand what the goal and process is.

Gerrit

#6

Updated by Jon Ambler about 7 years ago

I found out that they have already compared Dragen to GATK and BWA using the Platinum genomes trio, the accuracy and ROCs are found towards the bottom of this page.

http://edicogenome.com/pipelines/dragen-joint-genotyping-pipeline/

#7

Updated by Gerrit Botha about 7 years ago

Jon this message is from Nicky.

"Ok so the evaluation is done already. We need to decide if we need to make use of DRAGEN (assuming we get access), and what we will need it for."

Nicky, the Redmine IMAP scraper has some compatibility issues with the mail setup on mancala so tickets are not being populated by emails send. It is on my list to resolve but I'm kind of waiting for the CBIO mail server to be updated before spending to much time on this.

Gerrit

#8

Updated by Jon Ambler almost 7 years ago

  • % Done changed from 0 to 100

As testing has already been completed on a gold standard sample is reported above, closing this ticket to move to assessing data in-out pipeline.

#9

Updated by Jon Ambler almost 7 years ago

  • Status changed from New to Resolved

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