User: prosium

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prosium0
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Posts by prosium

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how to understand output form from CNVkit
... I've had 300 WGS matched samples and ran 'batch function' from CNVkit with command below. cnvkit.py batch WGS*Tumor.bam --normal WGS*Normal.bam --annotate refFlat_hg38.txt --fasta hg38.fa --output-reference ref.cnn --output-dir results --diagram --scatter -p 20 -m wgs output format is below ...
wgs cnv cnvkit written 8 months ago by prosium0
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Answer: A: Are Provean-SIFT-results consistent with SIFT-original-results?
... i got the error you said too. it's different sift-4G score and annovar-sift score. How would you do that? ...
written 15 months ago by prosium0
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Comment: C: I got a problem with making normal reference using cnvkit
... For the case-control sample, it is right to store all the samples in specific folder and run 'batch' according to the manual on the homepage. However, I can not afford to have a sufficient HDD usage, so first I use 'access' function as a ref genome and calculate coverage by using only normal sampl ...
written 16 months ago by prosium0
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I got a problem with making normal reference using cnvkit
... Hello, I am trying to use cnvkit with paired-WGS data and got an error with making normal reference. ---------- 1) $ cnvkit.py access hg19.fa -o access.hg19.bed ---------- 2) $ cnvkit.py autobin GroupA_Normal.bam -m wgs -g access.hg19.bed --annotate refFlat_hg19.txt $ cnvkit.py autobin Group ...
paired-wgs cnvkit normal-reference written 16 months ago by prosium0 • updated 16 months ago by Eric T.2.6k

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