User: sm.hashemin

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sm.hashemin90
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Posts by sm.hashemin

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Why there is a 50% variant allele frequency in TCGA NSCLC data?
... 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.hashemin90
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BAF without normal control, to do or not! or how
... 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 ...
cnvkit baf theta no controls theta2 written 4 months ago by sm.hashemin90 • updated 12 weeks ago by zhouyangyu0
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Comment: C: cnvkit bgzf_read error 4 after 4 bytes
... thanks for you answer. It says gzip compressed data, extra field ...
written 4 months ago by sm.hashemin90
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cnvkit bgzf_read error 4 after 4 bytes
... 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 ...
cnvkit samtools bzip written 4 months ago by sm.hashemin90 • updated 4 months ago by Eric T.2.5k
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Why there is a 50% variant allele frequency in TCGA NSCLC data?
... 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 ...
somatic tcga vaf snv variant alle frequency written 9 months ago by sm.hashemin90
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Comment: C: How to create a covariate file for MutSigCV using gene expression values from ot
... Having the same question here, did you find out where this value comes from? ...
written 9 months ago by sm.hashemin90
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Comment: C: Visualizing CNV data based from bed or bedgraph format
... 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.hashemin90
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Answer: A: Visualizing CNV data based from bed or bedgraph format
... 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.hashemin90
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Visualizing CNV data based from bed or bedgraph format
... 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 ...
R igv bedgraph cnv bed written 10 months ago by sm.hashemin90
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Comment: C: regions with very different VAF fall into one cluster
... Thanks a lot, you are a life saver. ...
written 10 months ago by sm.hashemin90

Latest awards to sm.hashemin

Scholar 4 months ago, created an answer that has been accepted. For A: Bcftools view. FREQ inclusion error.
Supporter 4 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Sciclone clonevol integration
Scholar 18 months ago, created an answer that has been accepted. For A: Bcftools view. FREQ inclusion error.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bcftools view. FREQ inclusion error.

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