[DOCKTESTERS] BWA-Mem update

Wed Mar 22 20:14:29 EDT 2017

I attached a PDF version of that page if you don't have access to our wiki.

George

From: Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>>
Date: Wednesday, March 22, 2017 at 4:14 PM
To: George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>>
Cc: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>>, 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

Excellent George, thanks! Those results are in accordance with what Jonas and I got from our tests for Sanger.

By the way, the link you sent does not seem to work for me.

Best

Miguel

On Wed, Mar 22, 2017 at 9:18 PM, George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>> wrote:
I finished one of the dockerized Sanger tests and upon verification there were just a few differences, but I'm not sure if they are normal or not.

Results:

root at dockstore-test3:~/PCAWG-Docker-Test# bin/compare_result.sh Sanger DO50398

var/spool/cwl/0/caveman/

var/spool/cwl/0/caveman/splitList

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.muts.ids.vcf.gz

var/spool/cwl/0/caveman/alg_bean

var/spool/cwl/0/caveman/prob_arr

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.snps.ids.vcf.gz.tbi

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.no_analysis.bed

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.snps.ids.vcf.gz

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.flagged.muts.vcf.gz

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.muts.ids.vcf.gz.tbi

var/spool/cwl/0/caveman/cov_arr

var/spool/cwl/0/caveman/7f94d650-41b9-4664-bcde-dc8533e4602d_vs_69586c55-6f81-4728-8a82-bd97bceafaaa.flagged.muts.vcf.gz.tbi

var/spool/cwl/0/caveman/caveman.cfg.ini

Comparison for DO50398 using Sanger

---

Common: 171325

Extra: 3

    - Example: 14:20031258:G,8:43827158:A,X:61711363:C

Missing: 13

    - Example: 10:106963148:T,17:64794691:G,1:82709263:T

Because I'm a infrastructure architect my main reason for the test was to monitor resource utilization, so I wrote a wiki detailing my observations:

https://wiki.oicr.on.ca/display/~gmihaiescu/Dockerized+Sanger+workflow

I have there more Docker tests running, two of them run Sanger against the same donor (but using Vms with 8 cores because I want to see if the run time and resource utilization are constant), and a third test that is running DKFZ.

Cheers,
George

From: Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>>
Date: Wednesday, March 22, 2017 at 1:08 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

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