[DOCKTESTERS] BWA-Mem update

[Miguel Vazquez]

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> 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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> Postdoctoral Researcher
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