User: sm.hashemin
sm.hashemin • 90
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Posts by sm.hashemin
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... Answering myself:
because mutations are considered to happen in heterozygous state, therefore at 100% purity you will have a 50% VAF. VAF of more than 50% belongs to the LOHs.
...
written 4 months ago by
sm.hashemin • 90
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... Dear Eric, dear all,
from the cnvkit documentation :
> Typically you would use a properly formatted VCF from joint tumor-normal SNV calling, e.g. the output of MuTect, VarDict, or FreeBayes, having already flagged somatic mutations so they can be skipped in this analysis. If yo ...
written 4 months ago by
sm.hashemin • 90
• updated
12 weeks ago by
zhouyangyu • 0
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... thanks for you answer. It says gzip compressed data, extra field ...
written 4 months ago by
sm.hashemin • 90
4
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... Hi, I am running CNVKIT and I am new to it. I was running a batch on two tumor samples with a flat reference.
anaconda3/bin/cnvkit.py batch 1.bam 2.bam -n -t /refseq_exome_genesymbol_headless_CNVkit.csv -f hg19.fasta --access access-5k-mappable.hg19.bed --output-reference my_flat_reference.cnn ...
written 4 months ago by
sm.hashemin • 90
• updated
4 months ago by
Eric T. • 2.5k
2
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... Hi,
I was taking a lot at the variant allele frequencies in TCGA NSCLC data (from the the MAF somatic SNV file). I have seen thet the highest VAF is 50% and it apears that they have a cutoff there. Does it mean that a SNV of 60% vaf can not be a homozygous mutations in 60% of cells (while tumor puri ...
written 9 months ago by
sm.hashemin • 90
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... Having the same question here, did you find out where this value comes from? ...
written 9 months ago by
sm.hashemin • 90
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... Thanks alot. I removed the zoom argument and the representation was a bit two detailed for an overview of genomic changes. Is the reperesentaion like this possible ?
https://us.v-cdn.net/5019796/uploads/FileUpload/58/15ca12b0618250b498391fe5562fb9.png ...
written 10 months ago by
sm.hashemin • 90
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3
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642
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... Thanks a lot for the answers I am more searching for a representation like the following.
As I have no normal samples I had to use ControlFREEC and reanalysis with another software is not an option.
![enter image description here][1]
[1]: https://us.v-cdn.net/5019796/uploads/FileUpload/58/15ca ...
written 10 months ago by
sm.hashemin • 90
4
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... Hi,
I was wondering if there is a package or script which may visualize multi-panel CNV just IGV does but with more flexibility from a cohort of bedgraph files? preferably in R? Sushi R package does not have a point based visualization otherwise might have been perfect.
Best
...
written 10 months ago by
sm.hashemin • 90
1
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... Thanks a lot, you are a life saver. ...
written 10 months ago by
sm.hashemin • 90
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For A: Bcftools view. FREQ inclusion error.
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created a question with more than 1,000 views.
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18 months ago,
created an answer that has been accepted.
For A: Bcftools view. FREQ inclusion error.
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For A: Bcftools view. FREQ inclusion error.
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