nhaus
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Activity overview
Latest activity by nhaus-
nhaus commented,
Hi Genevieve, Thank you very much for getting back to me so quickly. Honestly, I am still a bit puzzled by the results I am seeing. In the meantime I figured out what my problem was, and now every...
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nhaus created a post,
ApplyVQSR AS_FilterStatus=VQSRTrancheSNPXXXXtoXXXX but variant still passes FILTER
AnsweredHello, I am using GATK 4.2 to perform germline calling. To reduce the number of false positives, I use the VariantRecalibration workflow with the recommended resources. After using `ApplyVQSR` i...
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nhaus created a post,
VariantRecalibrator latest recommandations
AnsweredHello, I am currently trying to perform germline variant calling for human, however, I am somewhat stuck at the VQSR step. A big problem is, that all the links ("method documentation", "parameter r...
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nhaus created a post,
Panel of normals for Mutect2 GRCh37
Hello, I plan on using Mutect2 to call somatic variants for WGS. The alignment and sorting is already performed by the core facility, which uses the GRCh37.p13 reference genome. For optimal perform...
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nhaus created a post,
Panel of Normals from matched normals
AnsweredHey, I am planing to use Mutect2 to discover SNV/Indels. I read here that the panel of normals should be crated from "from subjects that were young and healthy to minimize the chance of using as no...
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nhaus created a post,
Using old VCF file for BaseRecalibrator
Hello, I want to use the BaseRecalibrator function and have the following question: I aligned my WGS to the GRCh38.p13. The problem is, that even after looking for hours I still can not find the db...