Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
Reputation:
18,180
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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Google Scholar Page
Last seen:
2 days, 10 hours ago
Joined:
7 years, 6 months ago
Email:
c***********@gmail.com

I work in the Genome Institute at Washington University in St. Louis, where I lead a group that develops and applies computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 969 results • page 1 of 97 • next >
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Answer: A: sciClone: usage for inferring tumor clonality
... 1) You should be using somatic calls, which means that you should only have one output file. (in your example, created from comparing the tumor and normal using varscan's somatic mode) 2) only three columns are required for the exclude file (chr, start, stop), and that's all that sciClone will look ...
written 4 days ago by Chris Miller18k
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Comment: C: How realible samtools/ bam-readcount /igvtools /pysamstats for finding deletions
... Another I've found useful is to remove variants from regions where at least 10% of reads have MQ 0. ...
written 9 days ago by Chris Miller18k
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Comment: C: How realible samtools/ bam-readcount /igvtools /pysamstats for finding deletions
... Yeah, it's very advisable. It includes lots of heuristic filters that remove junk calls. ...
written 11 days ago by Chris Miller18k
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Comment: C: Tumor purity estimation by allele frequency of COSMIC identified somatic mutatio
... Correct. See the recent [ISOWN paper](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0446-9), where they tried really hard to distinguish germline from somatic in tumor-only samples and still, lots of germline events slipped through. ...
written 16 days ago by Chris Miller18k
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Comment: C: Unable to access jarfile trimmomatic-0.35
... You don't have to make it, you need to download it from the trimmomatic site. If you have already downloaded it, you need to provide the path to that file. ...
written 16 days ago by Chris Miller18k
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Answer: A: Tumor purity estimation by allele frequency of COSMIC identified somatic mutatio
... And how will you know if those mutations are in the founding clone or a subclonal population? Or if they are copy-number altered, skewing their VAFs up or down, depending on which allele is lost? Or perhaps both CN-altered and Subclonal? Purity, ploidy, and copy number inference are all inextricab ...
written 16 days ago by Chris Miller18k
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Answer: A: Unable to access jarfile trimmomatic-0.35
... Is there a file in your current directory named "trimmomatic-0.35.jar"? If not, then you need to provide the full path to that file. ...
written 16 days ago by Chris Miller18k
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Answer: A: Unlisting lists inside data frame and collapsing their values in R
... My first thought is that you should examine your choices that got you to this point and choose a better data representation. If you *must* fix this problem as described, then something like this should work: for(i in 1:length(myDataFrame[,1])){ if(is.list(myDataFrame[i,3])){ ...
written 18 days ago by Chris Miller18k
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Comment: C: SomaticSniper: Depth of reads supporting variant(s) in normal =0
... Maybe check the sniper inputs - are there also base quality filters that might come into play? ...
written 27 days ago by Chris Miller18k
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Answer: A: sciClone: Multiple alleles at single position
... SciClone doesn't actually care what the position is, and it'd be a nice fix to change the code to reflect that (pull requests welcome). As a quick fix, though, I'd recommend just changing the sciclone inputs to something unique. if your variants look like: 1 123456 A/T 1 123456 A/C Th ...
written 6 weeks ago by Chris Miller18k

Latest awards to Chris Miller

Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Scholar 18 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Will Picard MarkDuplicates also un-mark duplicates?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 11 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Epic Question 3 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 3 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Popular Question 3 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 3 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

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