Tjitske de Vries
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Activity overview
Latest activity by Tjitske de Vries-
Tjitske de Vries created a post,
How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives
AnsweredMultiple mutations are filtered out as germline by filtermutectcalls, including very specific tumor hotspot mutations, often those mutations are located at a gain and have therefore a higher AF tha...
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Tjitske de Vries created a post,
Funcotator misses many Cosmic fields - update possible?
(REQUIRED) Please provide: a) GATK version used: 4.1.7.0b) Exact command used: gatk Funcotator --variant $file --reference $ref --ref-version hg19 --data-sources-path $db --output $out --output-fil...
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Tjitske de Vries commented,
Hi Genevieve Brandt, thank you for your response. I downloaded the GTF file as part of the bundle funcotator_dataSources.v1.7.20200521s.tar.gz from https://gatk.broadinstitute.org/hc/en-us/article...
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Tjitske de Vries created a post,
Funcotator datasources.v1.7 gencode raise error
(REQUIRED) For us to most effectively understand your question, please fill in your responses below: Hi, I tried to run Funcotator on my VCF file, for this I have downloaded the datasources v1.7 p...