Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
20,090
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
1 day, 4 hours ago
Joined:
8 years, 10 months ago
Email:
c***********@gmail.com

I work in the Division of Oncology and McDonnell Genome Institute at Washington University in St. Louis, where I develop and apply computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,080 results • page 1 of 108 • next >
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Answer: A: Does sciClone work on mouse exome data?
... I don't see why that wouldn't work, as long as there are enough somatic variants to track from the tumors. (Cluster confidence increases with number of variants and the depth of sequencing). ...
written 7 days ago by Chris Miller20k
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Answer: A: SciClone works with 1d clustering, but not 2d?
... Sorry that I missed this. You don't have your input vaf files formatted correctly. You have to actually merge your variant lists and get readcounts for each variant in all samples. (Not called is not the same as 0% vaf!) See this post (and several other under the sciclone tag) for more info. http ...
written 7 days ago by Chris Miller20k
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Answer: A: regions with very different VAF fall into one cluster
... You have not removed copy number altered variants from.your sample (this includes variants on sex Chris in males). Anything at 100% vaf is almost certainly in a CN1 region and needs to be excluded. See this post (and several others under the "sciclone" tag) for additional context https://www.biosta ...
written 7 days ago by Chris Miller20k
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Answer: A: Convert indel list with [-/A] notation to VCF with adjacent base
... One option seems to be converting to VEP format, with something like this: cut -f 1-5 $YOURFILE | perl -nae 'if($F[3] eq "-"){$F[2]=$F[1];$F[1]=$F[1]+1;};print join("\t",(@F[0..2],$F[3] . "/" . $F[4])) . "\n"' (assumes input is tsv like `chr1 123 124 - AA`) Then annotating with [VEP](htt ...
written 19 days ago by Chris Miller20k
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Convert indel list with [-/A] notation to VCF with adjacent base
... I couldn't find a previous answer to this question, but have to believe something exists! I'm trying to take a list of mutations that looks like this: chr1 120995 120996 -/TAT chr1 1090526 1090526 A/C chr1 2856178 2856178 G/C chr1 3975090 3975090 G/A chr1 44203 ...
vcf bed faidx convert written 19 days ago by Chris Miller20k • updated 18 days ago by finswimmer9.0k
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Answer: A: Cancer Genomics and Bioinformatics positions at WashU (Griffith Lab)
... I'm an active collaborator on several projects and can vouch that the Griffith Lab is a great place to work - fascinating research projects and good people! ...
written 4 weeks ago by Chris Miller20k
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Answer: A: Postdoc position in single-cell cancer genomics
... Just a note to say that I'm collaborating with Allegra on several projects, and it's a great environment, with a lot of exciting research going on, especially in the single-cell cancer genomics space. ...
written 4 weeks ago by Chris Miller20k
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Comment: C: Finding SNV showing allele specific bias
... You're going to have better luck getting useful answers if you a) show evidence that you've tried to research this problem yourself b) tell us what you've tried, and c) provide more details ...
written 5 weeks ago by Chris Miller20k
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Answer: A: Get Flanking Amino Acid Sequence
... Highly suggest that you check out the [pVACtools](https://pvactools.readthedocs.io/en/latest/) suite, which utilizes some VEP plugins and custom parsing to extract exactly this information and format it nicely prior to doing binding affinity predictions. ...
written 7 weeks ago by Chris Miller20k
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Answer: A: Getting same SNPs both in cancer and normal files when seen in IGV - Integrativ
... > To get SNPs specific to horn cancer, I have subtract Horn Normal vcf file from Horn Cancer vcf file using bedtools. Don't do this. The assumptions that germline variant callers make about VAF distributions and such don't lend themselves well to calling cancer variants. You need to use a true s ...
written 7 weeks ago by Chris Miller20k

Latest awards to Chris Miller

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 12 weeks ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 3 months ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 4 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
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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
Popular Question 8 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 11 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 13 months ago, created more than 1,000 posts (questions + answers + comments).

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