User: Zhenyu

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Zhenyu220
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Posts by Zhenyu

<prev • 53 results • page 1 of 6 • next >
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Comment: C: How to find On-Target and Off-Targer percentage of reads?
... We used HSmetics too. But some large WXS files have extreme memory requirement. Sometimes we have to double memory allocation from 16G to 32G, or even 64G to get this done. We don't see similar problems with WGSmetrics no matter how big the file is. Does anyone know alternatives of HSmetrics? ...
written 5 months ago by Zhenyu220
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Answer: A: WGS for TCGA HNSC project
... I don't know why the sequencesource will state otherwise, but if there is sdrf describing this vcf is derived from a WGS CGHub analysis_id/bam file, then it should be WGS. As to MAFs, ppl will not make project-level MAFs out of WGS calls given the file will be 100 times larger. ...
written 15 months ago by Zhenyu220
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Comment: C: tumor only variant calling tools
... Looks great, I will have a look. The panel of normals are expected to call CNV from target panels or WXS. ...
written 15 months ago by Zhenyu220
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Comment: C: tumor only variant calling tools
... Actually tumor only sample doesn't mean there is no normals. I may have overstated what FM is doing, but I really mean is that you can take advantages of tumor impurity, and make probability models if a variant is somatic or germline based on copy number variation, subclonality, and allele frequency ...
written 15 months ago by Zhenyu220
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Comment: C: tumor only variant calling tools
... hmmm. totally do not remember that post one year ago ...
written 15 months ago by Zhenyu220
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Comment: C: raw count on TCGA/GDC
... For GDC data, using the browser to select HTSeq count data, of your custom cohort, download the manifest, and use gdc-client to get them all. ...
written 15 months ago by Zhenyu220
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Comment: C: Differences between FPKM and FPKM-UQ files in gene expression analysis
... FPKM and UQ-FPKM are calculated by GDC just for legacy reason, because ppl used to use FPKM data, and UQ provides a method for normalization. However, for any serious analysis, using count data with DESeq/EdgeR are encouraged. ...
written 15 months ago by Zhenyu220
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tumor only variant calling tools
... I am looking for open source tools that can infer mutations from tumor sample without paired normal sample. I understand you can use tools like MuTect to do one sample calling, coupled with some filtering of common variants. But I am looking for some more complicated tools such as the one Foundatio ...
somatic ngs tumor mutation written 15 months ago by Zhenyu220
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Comment: C: How accurate is the IBD calculation by plink?
... Have you carefully QC'ed your genotypes like what you would do for GWAS analysis? Poor quality genotypes would give you wrong calculations, but it's not the fault of IBD. ...
written 19 months ago by Zhenyu220
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Answer: A: Any better ways to filter GATK Mutect2 output?
... hundreds of mutations may not be an indicator of bad data. Have you tried other callers and compare results together? ...
written 22 months ago by Zhenyu220

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