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Created 2013-10-01 00:55:10 | Updated 2013-10-01 14:24:41 | Tags: official 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:

http://www.appistry.com/news-and-events/appistry-webinar-which-mutations-matter


Created 2013-07-24 20:26:27 | Updated 2013-07-26 14:41:56 | Tags: official mutect appistry gatk webinar
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Heads up, cancer researchers! Appistry (our commercial licensing partner for GATK and now MuTect) is announcing an upcoming webinar on best practices for somatic mutation studies using GATK and MuTect. Registration for the webinar is open to all (not just Appistry customers) so be sure to sign up for this. See the announcement on Appistry's website for more detailed information.


Created 2015-05-15 01:23:27 | Updated | Tags: mutect
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I'm trying to build SomaticSpike, which is included in MuTect 1.1.4. Is there any way to actually build this from the github repository? Is there perhaps a binary floating around?


Created 2015-02-12 07:12:06 | Updated | Tags: indelrealigner baserecalibrator mutect
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Hello Do you recommened realign around indels and recalibrate quality score before running Mutect? Thanks!


Created 2014-05-23 16:41:17 | Updated | Tags: snpeff mutect
Comments (7)

I am interested to annotate using snpEff, only those somatic mutations that were flagged as 'KEEP' in the judgement call column of the *callstats file generated from muTect. I can see that these 'KEEP' calls (in the callstats file) are flagged as 'PASS' in the 'Filter' column of the corresponding VCF file.

I am now not sure if I should filter the VCF output files from Mutect (keep only the 'PASS' calls) for snpEff annotation. snpEff does the Ti/Tv ratios apart from functional annotation, so is it expected to provide snpEff the unfiltered VCF for accurate calculation of Ti/Tv ratio OR is it Ok to provide a filtered VCF with only the passed calls?

Thanks Parthav


Created 2012-11-05 19:45:35 | Updated | Tags: mutect gatk
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Hello, From a talk on MuTect from a while ago, I found a reference to filtering out "noisy" reads. This seems like a great idea, and I would like to do it for other standard GATK based variant calling as well. How exactly do you do this kind of "noisy read" filtering. From the graphic in the talk, it looks like reads with a lot of mismatches relative to the others in a region, after indel realignment are candidates for being these kind of noisy reads. How is this defined exactly though, and how could I do something similar with GATK? Thanks, John