Tagged with #cancer
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Created 2014-11-24 20:55:06 | Updated | Tags: jobs job-offer cancer

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We're advertising this job on behalf of our colleagues in the cancer analysis team. See the overview below the fold. If you're interested, please message me (@Geraldine_VdAuwera) or apply on the Broad's careers page (search for job requisition number 1591).

Please note that this job requires on-site presence (no remote work) and Broad cannot offer visa sponsorship for this opportunity.


Part-time opportunity to make a contribution to The Cancer Genome Atlas, a project with global impact in the search for a cure for cancer. Work with world-class researchers at the Broad Institute to publish large datasets generated by computational algorithms. Assist with development and maintenance of automated pipelines.

Part-time twice a week, on-site at the Broad Institute.

Characteristic Duties:

  • Assist cancer genome analysts in preparing data submissions to make available to the TCGA research community.
  • Generate automated data submissions for the TCGA research community.
  • Identify and address technical issues with automated pipelines.
  • Extend the functionality of automated pipelines.
  • Assist with documentation of automated pipelines.
  • Work with project managers to ensure that requirements and timelines are being met.
  • Work with engineers on process or design issues


  • Bachelor Degree or currently enrolled in a Bachelor Degree program. Computer Science, Computational Biology, or Bioinformatics preferred
  • Proficiency in linux or other unix flavor
  • Python experience a big plus
  • Knowledge of web services a plus
  • Prior involvement or interest in genomics a plus
  • Excellent communication skills

Created 2014-03-24 21:09:06 | Updated | Tags: support cancer

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I'm very happy to introduce Sheila Chandran, our newest GSA team member, who will be helping me with GATK outreach, support and documentation. You can expect to see Sheila start answering questions on the GATK forum within a week or two!

Thanks to Sheila's help, I'll be able to expand our support model to the Broad Cancer Tools (MuTect and related). Moving forward, we'll produce documentation for MuTect and other tools produced by the Cancer Group in collaboration with the developers, in order to bring you the same level of documentation coverage and support that we currently have for GATK.

Rest assured however that we won't stop working on improving the GATK documentation. In fact, Sheila's first project with us will be to document how the HaplotypeCaller works in detail -- something I know many of you have been hoping to see for a while now!

As a final note, I'd like to mention that this is one of many positive outcomes from our collaboration with our commercial licensing partner, Appistry, so we'd like to express our thanks to them for helping us help you, our user community.

Created 2013-10-01 00:55:10 | Updated 2013-10-01 14:24:41 | Tags: mutect appistry webinar cancer

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Our partner Appistry (who distribute GATK and MuTect to commercial users) will be holding a webinar on 3 October. Registration is open to all; you can find more details on the Appistry website here:


Created 2016-04-18 04:18:55 | Updated | Tags: cancer mutect2 somatic co-realingment

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I can't found the detail information of Co-realignment except for attached image.

  1. Could I get the improvment information of Co-realignment or detailed information?

  2. Can I processing the one BAM file (after Co-realingment, Normal and Tumor merged into one BAM) with Mutect2 for somatic call.

Created 2015-08-09 11:38:20 | Updated | Tags: best-practices dataprocessingpipeline cancer somatic-variants

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Hello, We're currently running a research project involving exome sequencing of tumors and paired normal blood samples from brain cancer patients. I'm relatively new to NGS processing but thanks to this forum (and the excellent documentation provided by the Broad) I was able to put together the following pipeline for this project: I just wanted to check with the Cancer Team that everything looks OK, as well as get any suggestions, if possible. Looking forward to your valuable response, -E

Created 2015-07-21 22:33:32 | Updated 2015-07-21 22:33:53 | Tags: workflow pipeline exome cancer

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I am new to Bioinformatics, and would like some advice on changes to the GATK workflow for cancer. I was told that the cancer workflow is different, and see that several different tools are available.

I have Exome data from tumor and normal. I have aligned them, and have BAM files for each sample. I am interested in identifying somatic variants.

The current workflow as I understand it is: -(Non-GATK) Picard Mark Duplicates or Samtools roundup -Indel Realignment (Realigner TargetCreator + Indel Realigner) -Base Quality Score Reacalibration (Base Recalibrator + PrintReads) -UnifiedGenotyper -Annotation using Oncotator (?) -MuTect (identify somatic mutations)

**My questions are:

  1. Is the above workflow reasonable/correct for what I'm trying to do?
  2. Is there any difference running samples one pair at a time, or running them all together? (I have 57 pairs. Should I do 57 runs of normal-tumor pairs, or 1 run of all 57 pairs?)**

Thank you, Gaius