[DOCKTESTERS] BWA-Mem update

Mon Apr 10 13:32:57 EDT 2017

Thank you for help guys.

I'll download the files using Miguel's "bin/download_unaligned.sh" script till for now, and use Jonas's updated BWA-Mem script tomorrow.

Cheers,
George

From: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>>
Date: Monday, April 10, 2017 at 12:33 PM
To: George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>>
Cc: Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>>, Keiran Raine <kr2 at sanger.ac.uk<mailto:kr2 at sanger.ac.uk>>, Junjun Zhang <Junjun.Zhang at oicr.on.ca<mailto:Junjun.Zhang at oicr.on.ca>>, "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>" <docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>
Subject: Re: [DOCKTESTERS] BWA-Mem update

Hi George,

We should be able to provide you with a final answer on this tomorrow by the latest :)
Would that be OK for you?

You could already download the relevant unaligned bam files as this will anyhow take some time.
Miguel and I have been running on donor DO51057 and you can find GNOS IDs for the unaligned files in the attached JSON file.
Get all of the bams defined under the “unaligned_bams” headers (there will be 2 of these headers in the JSON, one for the normal and one for the tumor).

The BWA-Mem docker is internally set to run on 8 cores, so using a large VM is unlikely to affect run-time.

Best wishes,
Jonas

_________________________________
Jonas Demeulemeester, PhD
Postdoctoral Researcher
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

T: +44 (0)20 3796 2594
M: +44 (0)7482 070730
E: jonas.demeulemeester at crick.ac.uk
W: www.crick.ac.uk

On 10 Apr 2017, at 17:11, George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>> wrote:

Hi,

I would like to run the BWA-mem dockerized workflow in the Collaboratory environment, but I need some help in order to do this:

  *   A ready-to-run script or instructions
  *   The input files: single file or multiple files, whatever the script needs as an input
  *   The donor ID, preferably the same donor that was already used in order to prove the reproducibility of the results

I can start the workflow on a large VM in order to speed up the result.

Also, I'm currently running the DKFZ workflow on DO50398 because I've already ran Sanger on it, and I want to compare the run times for the two workflows on the same data set.

Thank you,
George

From: Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>>
Date: Wednesday, March 22, 2017 at 2:08 PM
To: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>>
Cc: Keiran Raine <kr2 at sanger.ac.uk<mailto:kr2 at sanger.ac.uk>>, Junjun Zhang <Junjun.Zhang at oicr.on.ca<mailto:Junjun.Zhang at oicr.on.ca>>, George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>>, "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>" <docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>
Subject: Re: [DOCKTESTERS] BWA-Mem update

Thanks Jonas for this information.

I hope that someone here can provide us with some suggestion on what to try next. Perhaps the version issue that Jonas point out is the key.

I just want to add that, as I told Jonas earlier, my own tests using the new split BAM files also gave 3% mismatches.

Best regards

Miguel

On Wed, Mar 22, 2017 at 6:56 PM, Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>> wrote:
Hi all,

A brief update on the BWA-Mem docker tests.
I prepared normal + tumor lane-level unaligned bams for DO503011 and ran the BWA-Mem workflow for normal and tumor seperately.
Doing the comparison however, I am still getting 3% of reads that are aligned differently (see below for a few examples).
However, when checking the headers of the original and newly mapped bam files (attached) I noticed that the original is mapped using a different version of BWA and SeqWare.
I’m hoping the mapping differences can be ascribed to this.

Is there a list available somewhere detailing which samples were mapped using which versions?
That way we could select a relevant test sample without having to sort through the headers of all different bams.

Best wishes,
Jonas

newly aligned:

IDflagchrpos
HS2000-1012_275:7:1101:17411:15403993112743126
HS2000-1012_275:7:1101:17411:154031473112743376
HS2000-1012_275:7:1101:11883:83640991628672999
HS2000-1012_275:7:1101:11883:836401471628673223
HS2000-1012_275:7:1101:16576:28476163GL000238.121309
HS2000-1012_275:7:1101:16576:2847683GL000238.121664

vs the original:

IDflagchrpos
HS2000-1012_275:7:1101:17411:1540399854944243
HS2000-1012_275:7:1101:17411:15403147854944493
HS2000-1012_275:7:1101:11883:836401631628464362
HS2000-1012_275:7:1101:11883:83640831628464586
HS2000-1012_275:7:1101:16576:2847699126124549
HS2000-1012_275:7:1101:16576:28476147126124903

_________________________________
Jonas Demeulemeester, PhD
Postdoctoral Researcher
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

T: +44 (0)20 3796 2594<tel:+44%2020%203796%202594>
M: +44 (0)7482 070730<tel:+44%207482%20070730>
E: jonas.demeulemeester at crick.ac.uk
W: www.crick.ac.uk

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
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