[DOCKTESTERS] BWA-Mem update

[Keiran Raine]

Hi,

The jsonl files files on pancancer.org contain the versions of software used originally.  If someone can give me the BWA and bammarkduplicates(2?) versions used this may be explained.

Bammarkduplicates had a bug fix a few monthis into the mapping, but the reported differences at the time (I don't remember who did it) was <1%.

Keiran

From: Miguel Vazquez <mikisvaz at gmail.com>
Date: Wednesday, 22 March 2017 at 18:08
To: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk>
Cc: Keiran Raine <kr2 at sanger.ac.uk>, Junjun Zhang <Junjun.Zhang at oicr.on.ca>, George Mihaiescu <George.Mihaiescu at oicr.on.ca>, "docktesters at lists.icgc.org" <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:

ID flag chr pos
HS2000-1012_275:7:1101:17411:15403 99 3 112743126
HS2000-1012_275:7:1101:17411:15403 147 3 112743376
HS2000-1012_275:7:1101:11883:83640 99 16 28672999
HS2000-1012_275:7:1101:11883:83640 147 16 28673223
HS2000-1012_275:7:1101:16576:28476 163 GL000238.1 21309
HS2000-1012_275:7:1101:16576:28476 83 GL000238.1 21664

vs the original:

ID flag chr pos
HS2000-1012_275:7:1101:17411:15403 99 8 54944243
HS2000-1012_275:7:1101:17411:15403 147 8 54944493
HS2000-1012_275:7:1101:11883:83640 163 16 28464362
HS2000-1012_275:7:1101:11883:83640 83 16 28464586
HS2000-1012_275:7:1101:16576:28476 99 12 6124549
HS2000-1012_275:7:1101:16576:28476 147 12 6124903


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Jonas Demeulemeester, PhD
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The Francis Crick Institute
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