[DOCKTESTERS] Succesfull run of SV-Merge workflow, but no validation, on donors DO50311 and DO52526

Thu Apr 27 09:02:57 EDT 2017

Dear Miguel,

I’m glad it worked :).

The final sv-merge call set to compare with is the one linked out here https://wiki.oicr.on.ca/display/PANCANCER/Linkouts+to+Most+Current+PCAWG+Data pointing to this sv-merge file set:

https://www.synapse.org/#!Synapse:syn7596712

<https://www.synapse.org/#!Synapse:syn7596712>
The final SV-merge vcf files are named <aliquot_id>.pcawg_consensus_1.6.<date>.somatic.sv.vcf.gz and would be the ones to compare with DO52526.somatic.sv.vcf.gz from the Docker run.

Best

Francesco

On 27 Apr 2017, at 13.42, Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>> wrote:

Dear all,

I'm very pleased to announce that the SV-Merge workflow now runs succesfully thanks to the changes from Francesco Favero. You can read bellow the details if you are interested.

The next issue remaining is to validate these results against the official release. The files I have listed from ICGC for each donor are the following:

CNSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.svcp_1-0-3.20150120.somatic.cnv.vcf.gz
SGV.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-snowman.20151023.germline.indel.vcf.gz
SGV.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.dkfz-indelCalling_1-0-132-1-hpc.1510221331.germline.indel.vcf.gz
SGV.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.dkfz-snvCalling_1-0-132-1-hpc.1510221331.germline.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-snowman.20151023.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.consensus.20160830.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.consensus.20161006.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.dkfz-indelCalling_1-0-132-1-hpc.1510221331.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.dkfz-snvCalling_1-0-132-1-hpc.1510221331.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.MUSE_1-0rc-vcf.20151023.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.svcp_1-0-3.20150120.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.svcp_1-0-3.20150120.somatic.snv_mnv.vcf.gz
StGV.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-snowman.20151023.germline.sv.vcf.gz
StGV.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.embl-delly_1-0-0-preFilter-hpc.150715.germline.sv.vcf.gz
StSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-dRanger.20151023.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-dRanger_snowman.20151023.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.broad-snowman.20151023.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.embl-delly_1-0-0-preFilter-hpc.150715.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.131332b2-ff51-4bd7-a626-aff2ecea6135.svfix2_4-0-12.20160208.somatic.sv.vcf.gz

While the resulting files from the workflow are:

DO52526.log
DO52526.somatic.sv.bedpe
DO52526.somatic.sv_full.bedpe
DO52526.somatic.sv_full.vcf.gz
DO52526.somatic.sv_full.vcf.gz.tbi
DO52526.somatic.sv.stat
DO52526.somatic.sv.vcf.gz
DO52526.somatic.sv.vcf.gz.tbi
DO52526.sv.tar.gz

Is there a correspondence of files that I can check for differences?

Best

Miguel

On Thu, Apr 27, 2017 at 1:31 PM, Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>> wrote:
Hi Francesco,

Thank you very much for promptly resolving this issue. I can confirm that the workflow runs nicely and the outputs are also collected correctly. I'll update the wiki to reflect that the workflow runs successfully.

As with the filter workflows, the next issue is knowing what I need to compare this with to check if there were any differences with the official released file. Do you know?

Best regards,

Miguel

On Thu, Apr 27, 2017 at 12:10 PM, Francesco Favero <francesco.favero at bric.ku.dk<mailto:francesco.favero at bric.ku.dk>> wrote:
Hi Miguel,

I’ve added some text in the README in the git repo and slightly changed the behaviour of the tool to fix your problem.

We had to change the url of the docker container, as we moved the image to our docker-hub group account.

https://dockstore.org/containers/registry.hub.docker.com/weischenfeldt/pcawg_sv_merge
the stable version is 1.0.2 (it’s also the only one in dockstore so far)

We have tested it, and it works for our end. I hope it will get better for you as well.

The following is not a testing issue, but since Denis is in cc it's still useful to point it out:
I believe we need to change the tool name to end with “workflow", as for the guidelines.
I’m afraid to do so effectively, we need to change also the git repository name and/or the docker container image. Is that right?

Thanks

Best

Francesco

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