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Chris Miller

Chris Miller

Bioinformatics Grad student at Baylor College of Medicine. My online home is at
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Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease
RT @tomtomorrow: It's almost as if the linkage between employment and health care is a fundamentally terrible idea.
Maybe this will lead to the government just giving out birth control. Would be a nice first step towards single payer healthcare. #SCOTUS
"It is a good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast" - Konrad Lorenz
RT @michelledean: A startling bit, in which Alito basically says, “no worries, this applies only to women’s health”
RT @ACLU: Never before has #SCOTUS said employers can use their religious beliefs to deny employees a benefit they are guaranteed by law to receive.
RT @BorowitzReport: I worry that the US embracing soccer will lead to other things Europe does, like recognizing climate change and offering maternity leave.
RT @random_walker: Google Scholar should rename the "Recommended based on My Citations" page to "Papers that should cite my work but don't."
Want to live in a walkable area in STL? These are your options (and some are a stretch). Via
RT @matthewbaldwin: An easy way to get pizza sauce off the ceiling is to not have children. #lifehack
RT @GlennF: Maybe if a Republican senator found out one of his children was climate change.
bc it makes too much sense: "Why not share the cost of paying for roads in proportion to the usage made of roadways?"
Answer: A: Identifying the tumor clones and subclones with VAF from VarScan2 -
We built the sciClone package for exactly this purpose: It takes inputs of somatic mutations, with readcounts and VAFs, and uses that information to infer subclonal populations in heterogeneous tumors. It also gives you some nice visualization options. - Chris Miller
Comment: C: Will Picard MarkDuplicates also un-mark duplicates? -
Well played, sir.  In retrospect, doing the experiment myself would have been faster than that 10 minutes of searching and typing this post.  Thanks! - Chris Miller
Will Picard MarkDuplicates also un-mark duplicates? -
If I take a bam that's already aligned and has dups marked, remove a bunch of reads, then re-run Picard's mark-duplicates, will it correctly change the flags of reads that are no longer duplicates (but may have been before ditching the reads)? This question is proving surprisingly hard to google for. - Chris Miller
Vaccination works. Measles Incidence Rate Per 100,000 People, 1928 - 2003 (via
For all the policymakers that still don't get it: Building Bigger Roads Actually Makes Traffic Worse.
Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics? -
You also occasionally see IUPAC codes pop up in fasta sequences. - Chris Miller
Comment: C: How Can I Create A Protein-Protein Interface Schematic Or Diagram For Easy Viewi -
Nice detective work! That link didn't work for me, so I pointed it to the pubmed page - Chris Miller
Comment: C: CNV analysis tool on exome data for NGS -
Lots of answers in these previous questions.  (If there weren't a bunch of answers on this question already, I would have closed it as a duplicate) - Chris Miller
Comment: C: Best Cnv Software? -
Paired tumor/normal samples or single samples? (somatic or germline CNVs?) - Chris Miller
Comment: C: Convert A Matrix Into A Hash Of Arrays -
Not a bioinformatics question. Closing. - Chris Miller
Answer: A: How to make this kind of 3-D plotting for cancer subclones ? (picture attached) -
I'll put in a plug for our sciClone package, which produces some nice plots, though nothing exactly like you're showing here. - Chris Miller
Comment: C: Where I can download the program CNV-TV -
I agree - implementations are crucial. (And I've been pretty harsh in some reviews of papers that don't provide one). - Chris Miller
Answer: A: Tcga Lack Of Controls - Workarounds? -
It's often difficult to get appropriate matched normals for tumor methylation or expression data, as they'd have to be tissue-matched. If you're working with glioblastoma, you can't take a chunk of a patient's healthy brain. Same goes for blood cancers - it's really difficult to separate leukemic cells from non-leukemic cells and get a matched normal from the same patient. (for genomic DNA calls, you can just use non-proximal blood or skin) Your best bet is to find healthy samples of that tissue type from another source. I'd start with GEO, and would definitely consider pooling the normals to help smooth out differences specific to only one of your normal samples. Also beware of batch effects, since it's likely that different facilities generated the data. - Chris Miller
Answer: A: Comparing Exomes -How to get ALL variants -
What you probably want to do is call variants on both samples using standard parameters, merge and deduplicate the list of called sites, then get readcounts for each site from both samples. [bam-readcount]( is one tool that makes extracting this information easy. With that information, you can filter the results to your desired level of confidence, including the prior information that a variant was called in the other sample. - Chris Miller
Answer: A: Spliting a dataframe based in a chromosome -
There are many ways to do this. Here is one:   > a = data.frame(Chr=c(1,1,2,3),Position=c(1234,5678,3456,7890),LTR=c(2,3,4,5)) > a   Chr Position LTR 1   1     1234   2 2   1     5678   3 3   2     3456   4 4   3     7890   5 > for(i in unique(a$Chr)){write.table(a[a$Chr==i,],paste("newsplit",i,".txt",sep=""),sep="\t",quote=F,row.names=F)} - Chris Miller
Comment: C: Biostar 2.0, Second Beta, Help Us Test The New Site -
Possible solutions: 1) give the moderator the whole blurb of text up front and let them edit as they see fit (I think the template for a polite response is a good idea). 2) insert an intermediate step between the moderation form and posting, where the moderator can edit the auto-generated text block. 3) Include a polite note in a div with a slightly different color/font (think blockquote here) and let the moderator add text below it (thus preserving the separation between auto-text and my words). - Chris Miller
Answer: A: Which software should be used to get SNPs different from reference but same in a -
What you're looking to do is fairly straightforward. I'd just call SNPs with Samtools, then merge the lists with a little script. - Chris Miller
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