[DOCKTESTERS] BWA-Mem update

[Jonas Demeulemeester]

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


_________________________________
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

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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