Philipp Hähnel
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Activity overview
Latest activity by Philipp Hähnel-
Philipp Hähnel commented,
Hi Jiayi, are you interested in obtaining germline variants or somatic variants? For the former, HaplotypeCaller should be used, for the latter Mutect2. Are the disease and control samples patient-...
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Philipp Hähnel commented,
Hi Jiayi, if you mean by joint calling the multi-sample variant calling for Mutect2, then this is not done on a cohort basis, but on a per patient basis. The multi-sample calling pools evidence for...
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Philipp Hähnel commented,
Hi all, the gatk tools look for the index files at the same position where the feature file is located. Hence, the index files should be treated as hidden arguments in the command line prompt. The ...
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Philipp Hähnel commented,
Hi Balthasar, do you also see an adjacent multi-nucleotide variant TGGC>GGGG in the maf? I think Mutect2 chooses a reducible form of indels in the form of MNV + pure indel, here TGGC>GGGG plus G in...
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Philipp Hähnel commented,
Hi Robin, you can use MergeVcfs for merging the two PoN vcfs: gatk MergeVcfs -I pon1.vcf.gz -I pon2.vcf.gz -O merged_pon.vcf.gz Best, Philipp
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Philipp Hähnel commented,
Ranjan, This is almost correct. You'd run Mutect2 in paired tumor-normal mode with the normal sample from the adjacent normal tissue. Using the matched normal sample will filter rare germline vari...
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Philipp Hähnel commented,
Then you will want to create two panel of normals, one for each of those two subsets. If you want to be most accurate about the variant calling step, then use the respective PoN of the matching pla...
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Philipp Hähnel commented,
Dear Ranjan, you can use all blood samples, provided that they were sequenced on the same sequencing platform. The tumor samples should also be sequenced on that platform as the Panel of Normals is...
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Philipp Hähnel commented,
Dear Robin, based on the current best practices and version of the tools, the CalculateContamination part of the variant calling workflow is independent of calling the Mutect2 part. The contaminati...
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Philipp Hähnel commented,
Hi Simon, check your line breaks. You need additional \ to have unix not to recognize it as a line break. Best, Philipp