Moderator: Chris Miller
Chris Miller ♦ 20k
- Reputation:
- 19,580
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- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- Google Scholar Page
- Last seen:
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- Joined:
- 8 years, 5 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.
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Answer:
A: Sciclone took too long
... Are your 19k sites from exome or WGS? If the former, I suspect that something has gone horribly wrong with your mutation calling. In a decade of working on tumors, I've only seen a handful of MMR/POLE deficient cases with that kind of mutational burden in an exome.
Sciclone will also take a long ti ...
written 12 weeks ago by
Chris Miller ♦ 20k
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Answer:
A: Sciclone clonevol integration
... Yes, if clonevol doesn't come up with a valid consensus model, then it's impossible to plot that model. You should examine your results carefully to identify 1) artifactual calls that may result in clusters that are wrong (one class of reference-problem-induced FP tends to be at about 15% in every s ...
written 12 weeks ago by
Chris Miller ♦ 20k
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... Sciclone was written to assume that each variant's chr:pos would be unique. The simple workaround for collisions like this is just to give the second variant a different chrom and pos. (i.e. chr99 999999999). The places actual coordinates are used are for matching up variants with the CN regions to ...
written 12 weeks ago by
Chris Miller ♦ 20k
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Comment:
C: SciClone not numeric error
... You really should ask this as a top-level question, not buried in the comments of someone else's comment. Are your CN values log2? If so, then you need to set the appropriate "cnCallsAreLog2" parameter ...
written 3 months ago by
Chris Miller ♦ 20k
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... See: https://github.com/genome/somatic-sniper/issues/9 ...
written 3 months ago by
Chris Miller ♦ 20k
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... really nice solution! ...
written 3 months ago by
Chris Miller ♦ 20k
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371
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... Nope - the directory with the fasta and the indices was nuked. FWIW, I'm pretty sure that I can recreate this fastq by digging up the vector and gene sequences and spending an hour or two doing manual surgery. It just seems like there oughta be a better way! ...
written 3 months ago by
Chris Miller ♦ 20k
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... That gives each read in fasta format, not the entire contig.I guess that could be assembled in subsequent steps or something.. ...
written 3 months ago by
Chris Miller ♦ 20k
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6 follow
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... To make a long story short, I have a bam file that is aligned to the human reference plus a specific contig (human gene + viral vector introduced into a mouse).
The fasta file that was used for alignment got inadvertently deleted, but I have good coverage across the contig. Is there a straightfo ...
written 3 months ago by
Chris Miller ♦ 20k
• updated
3 months ago by
h.mon ♦ 18k
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... If given samtools input, copy cat will exclude chromosomes from depth normalization that appear to differ substantially from CN2, based on allele frequency information. This information is more coarse than what you'd get from programs like ABSOLUTE or TITAN_CNA, that use allele frequency but is a q ...
written 3 months ago by
Chris Miller ♦ 20k
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