User: biologist

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biologist10
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Posts by biologist

<prev • 5 results • page 1 of 1 • next >
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Weights in cnvkit cnr output
... Hello everyone, I have tried reading up on different biostars posts about cnvkit's cnr column weights but am still confused. From https://cnvkit.readthedocs.io/en/stable/pipeline.html, I understand that weights in .cnr are dependent on the size of the bin, deviation of the bin’s log2 value in the r ...
cnvkit written 9 weeks ago by biologist10 • updated 23 hours ago by Biostar ♦♦ 20
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Annotation of Pindel files using AnnotSV
... Hello everyone, After running pindel on a tumor-normal paired sample, I used pind2vcf to create one vcf with all the pindel information contained. Then I used AnnotSV to annotate my vcf. The command looks like this: $ANNOTSV/bin/AnnotSV -SVinputFile pindel.vcf -outputFile annotsv.vcf -txFile t ...
annotsv pindel written 10 weeks ago by biologist10
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Comment: C: Passing cnvkit output to pureCN to account for cellularity
... Hi Markus, Thank you for your detailed response. I would like to clarify some things: 1) For the first command, you mentioned that PureCN accepts CNVkit coverage files. Does this mean a .cnr or .cns file from cnvkit? (Sorry for the basic question but I wasn't exactly sure what a coverage file was h ...
written 11 weeks ago by biologist10
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Passing cnvkit output to pureCN to account for cellularity
... Hello all, I have a question about how to pass cnvkit's output to pureCN to account for the tumor cellularity, According to https://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/Quick.pdf, Page 6 I first do: Rscript $PURECN/NormalDB.R --outdir $OUT_REF --normal_panel $NORM ...
cnvkit purecn written 12 weeks ago by biologist10 • updated 12 weeks ago by markus.riester480
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Problems wth cnvkit scatter for genes
... Hello, I have a .cnr and .cns file from cnvkit after running it on a tumor-germline paired sample. I would like to plot genes to see the cnvs per exon if possible and so I am using the cnr file to do this. These are some of my rows from the .cnr file for PTEN: > chromosome start end gene ...
cnvkit written 3 months ago by biologist10 • updated 3 months ago by h.mon26k

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