User: thondeboer

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thondeboer40
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Posts by thondeboer

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Answer: A: Merge multiple VCF files (same variants, same sample) into one VCF file
... Seems that CombineVariants is no longer part of GATK4 and the closest tool in GATK 4 is MergeVcfs, but that is not smart and simply creates duplicate lines and does not merge the annotations...Sorry... ...
written 24 months ago by thondeboer40
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Answer: A: Merge multiple VCF files (same variants, same sample) into one VCF file
... I think GATK's CombineVariants can do this...I have the same issue but have not confirmed this yet. https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php And now GATK is going to be Open Source, you should be a ...
written 24 months ago by thondeboer40
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Finding the Nucleotides inserted in a COSMIC entry in the CosmicCompleteExport file
... I am looking at a specific cosmic mutation that has a section called “Nucleotides inserted” when I look at the entry on the website, but when I look in the download file “CosmicCompleteExport” I don’t see a field with the inserted sequence: Web view http://cancer.sanger.ac.uk/cosmic/mutation/overv ...
cosmic written 4.9 years ago by thondeboer40 • updated 4.8 years ago by Biostar ♦♦ 20
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Comment: C: Best/most common file format for CNV data
... Looking into this some more, I guess it only is a database of regions of variations. Each study/sample will have a different CN associated with this ofcourse... So, what I am looking for is the actual study data I think...Looking some more ...
written 4.9 years ago by thondeboer40
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Comment: C: Best/most common file format for CNV data
... Well..It may be a subset, but there is no information in the few entries you showed of the actual SIZE of the copy number. I downloaded the GVF for the somatic mutations and none of the entries in the GVF file seem to have any information about the actual copy number of the region..Or am I missing ...
written 4.9 years ago by thondeboer40
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Answer: A: Best/most common file format for CNV data
... Thanks for the help, but it is clear that there is not much of a standard out there...Other then shoehorning it into VCF or GVF with its own set of attributes...But I guess that is we'll have to do... BTW...It's not clear to me what the CNV is in the GVF format...it only seems to indicate that ther ...
written 4.9 years ago by thondeboer40
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Best/most common file format for CNV data
... Hi,   We are developing some software with our Archer NGS kits that produces some CNV data and I was wondering what the best (or, more appropriately, most common) standard data file format is for CNV data? I hate to invent YAF (Yet Another Format) since we are already drowning in data file formats ...
data format cnv written 4.9 years ago by thondeboer40 • updated 4.9 years ago by Chris Miller21k

Latest awards to thondeboer

Popular Question 24 months ago, created a question with more than 1,000 views. For Finding the Nucleotides inserted in a COSMIC entry in the CosmicCompleteExport file
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Best/most common file format for CNV data
Student 4.5 years ago, asked a question with at least 3 up-votes. For Best/most common file format for CNV data

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