User: syntax

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syntax50
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Posts by syntax

<prev • 21 results • page 1 of 3 • next >
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How rare are somatic mutations?
... 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 ...
varscan tumor mutect snp somatic written 4 weeks ago by syntax50
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Comment: C: Are SV tools as thorough in CNV detection as CNVkit?
... Oh, GATK4 is introducing germline and somatic CNV detection that outputs to vcf. ...
written 3 months ago by syntax50
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Are SV tools as thorough in CNV detection as CNVkit?
... 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 ...
sv cnvkit parliament manta cnv written 3 months ago by syntax50
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Comment: C: VCF - what are overlapping variants?
... 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 syntax50
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Comment: C: Are small insertions always single-stranded?
... Wow. So a matching nucleotide will likely be inserted on the other side? Thanks! ...
written 4 months ago by syntax50
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Are small insertions always single-stranded?
... 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 ...
indel written 4 months ago by syntax50
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Comment: C: VCF - what are overlapping variants?
... 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 syntax50
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VCF - what are overlapping variants?
... 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 ...
vcf written 4 months ago by syntax50 • updated 4 months ago by Pierre Lindenbaum124k
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Comment: C: VCF - does mother or father come first in the comma separated ALT
... 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 syntax50
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Comment: A: VCF - does mother or father come first in the comma separated ALT
... 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 syntax50

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