User: syntax

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syntax60
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Posts by syntax

<prev • 24 results • page 1 of 3 • next >
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How do BOLT and SAIGE calculate LD?... with PLINK LD?
... When you run a PLINK GWAS, you run PLINK LD on the significant hits. How is LD calculated for other association algorithms like BOLT and SAIGE? ...
gwas bolt saige plink written 12 months ago by syntax60
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Comment: C: Noncoding annotations for WGS?
... Thank you. I'm having a look now. What kinds of questions would this help you answer about a gene or variant? ...
written 13 months ago by syntax60
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Noncoding annotations for WGS?
... When looking at SNV and CNV in intronic regions, what annotations should be taken into account? Here is what I can think of so far: - Histone regions - Regulatory sites (splicing) - Transcription factors - eQTL catalogs (GTEx, Expression Atlas) ...
annotation noncoding intron written 13 months ago by syntax60
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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 15 months ago by syntax60
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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 17 months ago by syntax60
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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 17 months ago by syntax60
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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 19 months ago by syntax60
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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 19 months ago by syntax60
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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 19 months ago by syntax60 • updated 10 weeks ago by Biostar ♦♦ 20
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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 19 months ago by syntax60

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Popular Question 13 months ago, created a question with more than 1,000 views. For Workflows! Where is the code?
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