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 14 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 14 months ago by
sm.hashemin • 90
• updated
12 months ago by
zhouyangyu • 0
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... thanks for you answer. It says gzip compressed data, extra field ...
written 14 months ago by
sm.hashemin • 90
4
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570
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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 14 months ago by
sm.hashemin • 90
• updated
14 months ago by
Eric T. • 2.6k
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 18 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 19 months ago by
sm.hashemin • 90
0
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3
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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 19 months ago by
sm.hashemin • 90
0
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3
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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 19 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 19 months ago by
sm.hashemin • 90
1
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1
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469
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... Thanks a lot, you are a life saver. ...
written 20 months ago by
sm.hashemin • 90
Latest awards to sm.hashemin
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14 months ago,
created an answer that has been accepted.
For A: Bcftools view. FREQ inclusion error.
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14 months ago,
voted at least 25 times.
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Sciclone clonevol integration
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Bcftools view. FREQ inclusion error.
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: Bcftools view. FREQ inclusion error.
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