User: tanbiswas6

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tanbiswas60
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Posts by tanbiswas6

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Copy number axis in sequenza result files are not fully resolved.
... Hi I've used sequenza to infer CNV profile from WES data. However, in the pdf files which I got from sequenza analysis, the copy number axis is not fully resolved. Please see the following chromosome 1 plot in which the bottom plot is not easily understandable. Can anyone please tell me what is ...
sequenza cnvs written 7 months ago by tanbiswas60
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Comment: C: CNVKit noisy scatter plot
... Yes, I've the bed file which have the coordinates. I used that file to make my target file for CNVkit. I'll follow the link. Okay, Thank you. ...
written 8 months ago by tanbiswas60
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Comment: C: CNVKit noisy scatter plot
... Hi Eugene 1. So, you are suggesting to build a reference file using PON? I had generated pon using 7samples during gatk pipeline to call SNVs. will that be okay if I use those 7samples to generate a CNV reference file in CNVkit? or you are suggesting to download more normal WES sample and then gene ...
written 8 months ago by tanbiswas60
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Comment: C: CNVKit noisy scatter plot
... Hi Eric 1. I'm processing my tumor samples with a matched normal samples. I'm using re-calibrated bam (recal.bam) files as an input. First I used the target command with -annotate and --short names to generate mytargets_short_names.bed file. Then I used the batch command with this target file. 2. I ...
written 8 months ago by tanbiswas60
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Comment: C: Whole Exome CNV tools
... Hi ReWeeda, I've used FREEC and CNVkit to analyze CNV profile fro WES tumor samples. In both cases the output profile looked noisy. Please see these links: 1) CNVkit problem: https://www.biostars.org/p/437788/#438015 2) FREEC: https://www.biostars.org/p/416986/ Please suggest something. Can I use ...
written 8 months ago by tanbiswas60
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Comment: C: CNVKit noisy scatter plot
... Could you suggest any? ...
written 8 months ago by tanbiswas60
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Comment: C: CNVKit noisy scatter plot
... This for only one tumor sample and after getting this sequencing data I checked for its quality and it was very nice. We also used this sample to identify indels and SNVs using GATK pipeline. That time we didn't have any problem. Only to identify CNVs, this data looks noisy. I don't know where is my ...
written 8 months ago by tanbiswas60
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CNVKit noisy scatter plot
... Hi, I'm using WES data of tumor samples to find out CNV using CNVkit. My input data was re-calibrated BAM (recal.bam) files for CNVkit. I've used CNVkit's batch command (https://cnvkit.readthedocs.io/en/stable/pipeline.html) to generate CNV profile. The output looks like this. Then I used ...
cnvkit copy number profile cnv on wes data cnv written 8 months ago by tanbiswas60 • updated 8 months ago by Eugene A90
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Preparing pyclone input files
... Hi I've vcf files and now want to do pyclone analysis. can anyone suggest how can I generate input files for pyclone from vcf files? ...
pyclone vcf file pyclone input written 9 months ago by tanbiswas60
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Comment: C: CNV Profile figure
... This WES data and ControlFC does segmentation itself. But still that data looks so noisy. That's why can't interpret it. I've used sorted BAM files (created using GATK best practice pipeline) as an input for ControlFC. ...
written 12 months ago by tanbiswas60

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