[DOCKTESTERS] BWA-Mem update

[Miguel Vazquez]

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> 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>
> Date: Wednesday, March 22, 2017 at 1:08 PM
> 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> 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 <+44%2020%203796%202594>
>> M: +44 (0)7482 070730 <+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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