User: syntax
syntax • 50
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Posts by syntax
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... In Foundation Medicine's Tumor Mutation Burden (TMB) study...
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2
They claim a **median of 3.6 somatic mutations per Mb (million)** in metasticised samples. Despite the fact that the experiment filtered out germline and dbSNP v ...
written 4 weeks ago by
syntax • 50
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... Oh, GATK4 is introducing germline and somatic CNV detection that outputs to vcf. ...
written 3 months ago by
syntax • 50
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... In reading through the documentation of tools like Illumina Manta, DNAnexus Parliament, Delly, Mobster - they make reference to CNV as one of the types of structural variation that can be detected.
However, when I read through CNVkit's documentation it is extremely thorough and specific to amplifi ...
written 3 months ago by
syntax • 50
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... Thanks for the explanation, Len. Seems like computer scientists trying to save a few bits.
I'm sure I will be running that tool of yours soon enough. ...
written 4 months ago by
syntax • 50
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... Wow. So a matching nucleotide will likely be inserted on the other side? Thanks! ...
written 4 months ago by
syntax • 50
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... Are small insertions (indels) always single stranded?
In the example below a break in the lower strand is repaired with the insertion of G. It could have inserted more than 1 nucleotide though.
Is it true that small insertions would never insert on both strands... as seen in large-scale SV inserti ...
written 4 months ago by
syntax • 50
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... Thanks Pierre. Please allow me to clarify as I am not all the way there yet.
Guessing your 4th column is ALT and the 5th column is REF.
CAGA represents a 4-nucleotide insertion? And the last A in that insertion is falls at position 13462... where it is being counted a second time as a snp?
Looke ...
written 4 months ago by
syntax • 50
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... As referenced in the pvcf documentation… what are overlapping variants?
https://www.biorxiv.org/content/biorxiv/early/2018/06/11/343970.full.pdf
> **Hybrid allelic representation.** To facilitate
downstream summary statistics without doublecounting, ideal unified sites would be completely nonove ...
written 4 months ago by
syntax • 50
• updated
4 months ago by
Pierre Lindenbaum ♦ 124k
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... I guess if ploids are split and read one at a time... the first position would at least always correspond to the same sequence for the length of the read?
But how can you trust a codon type when you don't know what sample comes from what index order in the alt column?
https://en.wikipedia.org/wiki/ ...
written 4 months ago by
syntax • 50
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... I guess if ploids are split and read one at a time... the first position would at least always correspond to the same sequence for the length of the read?
But how can you trust a codon type when you don't know what sample comes from what index order in the alt column?
https://en.wikipedia.org/wiki/ ...
written 4 months ago by
syntax • 50
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