User: ww22runner

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ww22runner0
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Posts by ww22runner

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Comment: C: Calling somatic variants with Varscan
... That makes sense, thank you for your advice. ...
written 5 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 5 months ago by ww22runner0 • updated 5 months ago by RamRS20k
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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 5 months ago by ww22runner0
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Comment: C: Calling somatic variants with Varscan
... thank you for your input. ...
written 5 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 5 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 5 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 6 months ago by ww22runner0
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Comment: C: Read Name in IGV and duplicates
... Hi finswimmer, Thank you for your reply. When we use Picard's MarkDuplicates tool, it has an option, Remove Duplicates that I set to true. Would this not remove the duplicates? ...
written 6 months ago by ww22runner0
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Read Name in IGV and duplicates
... Hello everyone, I have a question regarding IGV. When we select a read in particular and look at a SNP, we can view different metrics such as read name, sample, read group etc (https://bioinformatics-ca.github.io/images/Igv_click_read.png ). Could anyone tell me what exactly read name is? I am ask ...
igv written 6 months ago by ww22runner0 • updated 6 months ago by finswimmer11k
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Comment: C: Reading in delta Ct values using HTqPCR
... Thanks Kevin, I shall do that. ...
written 13 months ago by ww22runner0

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