Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
20,470
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
9 years, 3 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 • 1,095 results • page 2 of 110 • next >
1
vote
0
answers
321
views
0
answers
Job: Bioinformatics Developer/Analyst - Washington University in St. Louis
... Our cancer genomics team is expanding by adding additional analysts and developers. You'll join a well-established group of computationally-savvy researchers working on cutting edge questions in the field. This group, under the Genomics of AML Program Project Grant, sequenced the first human cancer ...
job wustl written 3 months ago by Chris Miller20k
0
votes
0
answers
1.3k
views
0
answers
Comment: C: Visualize VarScan2 Copy Number Aberrations in IGV
... The primary issue is that most copy number events are of size megabase or more. IGV works best on the base-to-kilobase scale. You certainly can make bed-like tracks that show your CN event, but it's probably not going to be the most helpful view.. ...
written 4 months ago by Chris Miller20k
3
votes
3
answers
394
views
3
answers
Answer: A: Reproducing this picture
... GenVisR is a good R package for this, as is ProteinPaint from St Jude: https://pecan.stjude.cloud/proteinpaint ...
written 4 months ago by Chris Miller20k
0
votes
1
answer
181
views
1
answers
Comment: C: Detecting known, low frequency SNPs in bacterial populations
... The output is specified in the readme here: https://github.com/genome/bam-readcount It gives you counts of each base at that position, along with some extra qc information (on quality, strand bias, etc) You will have to look at those numbers and formulate a way to set a minimum level of detection ...
written 4 months ago by Chris Miller20k
1
vote
1
answer
181
views
1
answers
Answer: A: Detecting known, low frequency SNPs in bacterial populations
... - As noted above, the parameters for varscan matter a lot. Relaxing them substantially will probably be helpful - If you have known positions, you can just use [bam-readcount](https://github.com/genome/bam-readcount) to query those directly, then apply whatever post-hoc filtering or statistics you ...
written 4 months ago by Chris Miller20k
1
vote
1
answer
324
views
1
answers
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 5 months ago by Chris Miller20k
0
votes
1
answer
243
views
1
answers
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 5 months ago by Chris Miller20k
1
vote
1
answer
229
views
1
answers
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 5 months ago by Chris Miller20k
0
votes
3
answers
278
views
3
answers
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 5 months ago by Chris Miller20k
1
vote
3
answers
278
views
3
answers
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 5 months ago by Chris Miller20k • updated 10 weeks ago by or.yaacov0

Latest awards to Chris Miller

Great Question 12 days ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 27 days ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 4 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Epic Question 4 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 7 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 7 months ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 8 months ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 8 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 9 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2026 users visited in the last hour