[DOCKTESTERS] sv-merge parameter questions

[Miguel Vazquez]

Thanks Denis for putting us in contact.

If it helps here is a list of the files I find in the ICGC DCC for a
particular donor (in format $type.$specimen.$filename)

CNSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.dkfz-copyNumberEstimation_1-0-189.20150817.somatic.cnv.vcf.gz
CNSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.svcp_1-0-5.20150701.somatic.cnv.vcf.gz
SGV.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-snowman-10.20151223.germline.indel.vcf.gz
SGV.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.dkfz-indelCalling_1-0-132-1.20150817.germline.indel.vcf.gz
SGV.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.dkfz-snvCalling_1-0-132-1.20150817.germline.snv_mnv.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-snowman-10.20151223.somatic.indel.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.consensus.20160830.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.dkfz-indelCalling_1-0-132-1.20150817.somatic.indel.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.MUSE_1-0rc-b391201-vcf.20151223.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.svcp_1-0-5.20150701.somatic.indel.vcf.gz
SSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.svcp_1-0-5.20150701.somatic.snv_mnv.vcf.gz
StGV.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-snowman-10.20151223.germline.sv.vcf.gz
StGV.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.embl-delly_1-3-0-preFilter.20150817.germline.sv.vcf.gz
StSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-dRanger-10.20151223.somatic.sv.vcf.gz
StSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-dRanger_snowman-10.20151223.somatic.sv.vcf.gz
StSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.broad-snowman-10.20151223.somatic.sv.vcf.gz
StSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.embl-delly_1-3-0-preFilter.20150817.somatic.sv.vcf.gz
StSM.Primary tumour - solid
tissue.2ea2294d-fab9-43ae-a222-370487495b06.svfix2_4-0-12.20160208.somatic.sv.vcf.gz


On Mon, Apr 17, 2017 at 3:57 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> Hi,
>
>
> Miguel is currently testing out the sv-merge workflow  (
> https://bitbucket.org/weischenfeldt/pcawg_sv_merge) with real data (as
> opposed to the testing data in https://bitbucket.org/
> weischenfeldt/pcawg_sv_merge/src/ced14ae88a2fbfb7274eb71834121d
> ca0de81236/Dockstore.json?at=docker&fileviewer=file-view-default )
>
>
> I believe that he has some questions about where to find the vcf parameter
> files on either the icgc-portal or on GNOS for a particular donor. Could
> either of you shed some light on this? Thanks!
>
>
> *Denis Yuen*
> Senior Software Developer
>
>
> *Ontario* *Institute* *for* *Cancer* *Research*
> MaRS Centre
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