User: ww22runner

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ww22runner0
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Posts by ww22runner

<prev • 20 results • page 1 of 2 • next >
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Comment: C: CNVKIT - unable to produce scatter and diagram pdfs
... Hi Steve, Thank you for your input and advise! I could run this script using Python 2 with the same bed file without issues but have been facing problems ever since I switched over to Python3. Nonetheless, I will refer to your pipeline to better understand how I could be running cnvkit. ...
written 4 months ago by ww22runner0
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Comment: C: CNVKIT - unable to produce scatter and diagram pdfs
... Hi Steve, I might be mistaken but I send in my target regions (baits) as a bed file to --targets. I see the message above for all of my tumor samples and had initially understood this as since anti target sites are not targeted sites, there is little/no coverage there. Should I be doing something di ...
written 4 months ago by ww22runner0
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CNVKIT - unable to produce scatter and diagram pdfs
... Hello everyone, I have a couple of tumor-germline paired samples and I tried running cnvkit this way: cnvkit.py batch *Tumor.bam --normal *Normal.bam \ --targets my_baits.bed \ --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \ --output-reference my_refer ...
cnvkit written 5 months ago by ww22runner0 • updated 4 months ago by Eric T.2.5k
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Comment: C: Calling somatic variants with Varscan
... That makes sense, thank you for your advice. ...
written 13 months ago by ww22runner0
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Problem understanding GT from Varscan's vcf output
... Hello all, I am trying to look for somatic variants in paired tumor/normal samples and have been using Varscan's somatic and processSomatic commands to obtain a vcf. However, I am having trouble understanding the output. For somatic variants called with high confidence, an example is: > #C ...
varscan written 13 months ago by ww22runner0 • updated 13 months ago by RamRS25k
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Comment: C: Calling somatic variants with Varscan
... Hello ATpoint, Thank you for your input. I have also been doing something along the same lines (somatic > processSomatic) to look at somatic variations but was wondering how different the results may be if I took approach 1 instead. Would the results be mostly similar? I am trying to switch over ...
written 13 months ago by ww22runner0
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Comment: C: Calling somatic variants with Varscan
... thank you for your input. ...
written 14 months ago by ww22runner0
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input for Pindel
... Hello all, This may be a basic question but for the config file in Pindel, do we provide the absolute path to both the normal sample bam as well as the tumor bam files in the event that we have tumor normal pairs? Thanks! ...
pindel written 14 months ago by ww22runner0
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Calling somatic variants with Varscan
... Hello everyone, I am trying to use Varscan to find somatic variants but I want to apply filters on the minimum variant frequency and minimum number of variant reads. I have tumor-normal paired samples. In this case, should I use: a) mpileup2snp and mpileup2indel separately and indicate the filters ...
varscan written 14 months ago by ww22runner0
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Comment: C: Read Name in IGV and duplicates
... Thank you WouterDeCoster, will use this in future posts. ...
written 14 months ago by ww22runner0

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