David Roazen
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Activity overview
Latest activity by David Roazen-
David Roazen commented,
I have edited the title and opening paragraph of this article to make it clear that GATK 4.6 reverts the behavior described here and switches back to the standard ./. representation for no-calls in...
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David Roazen commented,
Hi Thomas Stevens, Do you have the gnomAD datasource activated (see https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial#1.1.2.2)? The gnomAD datasourc...
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David Roazen commented,
(Answered in the user's other thread here: https://gatk.broadinstitute.org/hc/en-us/community/posts/24087106721051-Funocator-chromosome-missmatch-to-somatic-variant-calling-pipeline)
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David Roazen commented,
Hi Thomas Stevens, The message about "The following contigs are present in b37 and missing in the input VCF sequence dictionary" is just Funcotator's confusing way of telling you that your input VC...
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David Roazen commented,
Hi Smilesky, This pipeline is published here: https://github.com/broadinstitute/TAG-public/tree/master/Liquid_Biopsy_Duplex_Analysis It is still in use, however it is close to being retired, and so...
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David Roazen commented,
Hi Gongyuan Cao, This message is no cause for concern. It just indicates that a GenomicsDB operation took slightly longer than usual, but otherwise completed normally. Regards, David
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David Roazen commented,
Hi Arman Seuylemezian, The vcfheader.vcf file is just used internally for bookkeeping purposes by GenomicsDB to store VCF header metadata, and does not contain any sample information. When you use ...
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David Roazen commented,
Hi Arman Seuylemezian, Yes, the callset.json file contains the list of samples currently in the datastore. When incrementally adding more samples to an existing GenomicsDB, it's important to keep t...
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David Roazen commented,
Hi Maria G, Can you please confirm that the .dict file is in the location where GATK expects it to be (/storage/home/hcoda1/8/mgranada3/scratch/Reference/C_glabrata_CBS138_current_chromosomes.dict)...
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David Roazen commented,
This change was originally made to allow our joint calling pipeline to scale to handle the hundreds of thousands of samples in the AllOfUs project. I agree that it's problematic and confusing for d...