User: user56

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user56290
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informatics

Posts by user56

<prev • 37 results • page 1 of 4 • next >
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How can I download the whole ClinVar database
... Imagine a pipeline that interprets VCF file findings for a clinician. How can a user download (for offline use) the complete ClinVar database. (specifically, what is needed is a column that somehow indicates clinical level of evidence for each variant - e.g., level 1 (important, validated clinical ...
next-gen written 3.5 years ago by user56290 • updated 16 months ago by Biostar ♦♦ 20
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Comment: C: Tool To Generate Proportional Venn Diagrams?
... both links to Dropbox are broken! ...
written 4.9 years ago by user56290
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1
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Comment: C: What Is The Expected Size Of A Whole Genome Vcf And Bcf?
... VCF file can have more than one patient in it, are you talking a single patient? If more, then it will affect the size. ...
written 5.1 years ago by user56290
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What The The Most Commonly Used Databases For Clinical Annotation Of Genomic Results?
... Assume there is a patient or patients for which you have WGS or genotyping results. What are the most commonly used databases where you can get reliable clinical annotations (clinical impact) of each observed short variant. Examples are HGMD (Human Genome Mutations database), dbSNP (limited clinic ...
annotation written 5.1 years ago by user56290 • updated 5.1 years ago by Matt Shirley7.9k
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Comment: C: What Is European Counterpart Of Clia Certification?
... Bioinformatics tools are part of the pipeline that generates genetic testing resutls and that get the CLIA stamp or approval. I think it IS relevant. By using wrong methods you produce wrong data. Using correct pipeline is very important. ...
written 5.2 years ago by user56290
6
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Would You Like To Have A Reference Sequence - Would It Be A Healthy/Desirable Genome?
... Assume you would sequence yourself and by some immaculate chance you would have exactly the GRCh37 sequence. How the reference sequence is constructed ? I assume that with input from more and more Europeands, the European version of the reference sequence should have the most frequent allele in mos ...
written 5.2 years ago by user56290 • updated 3.7 years ago by Biostar ♦♦ 20
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Vcf And Copy Number Variations - How These Could Be Displayed?
... This is a newbie questions. Assume I have a VCF file with 69 people. I can see all short in[/]dels, in addition to SNPs. (nice improvement over genotyping) But the genomes of the patients also have CNVs. The DNA is huge and I only see differences in the VCF to the reference genome. Can the VCF fi ...
vcf cnv written 5.2 years ago by user56290 • updated 5.2 years ago by Ryan D3.2k
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(Closed) What Is European Counterpart Of Clia Certification?
... In US, a lab doing genetic testing must be CLIA certified. Is there any regulation similar to CLIA in Europe? ...
written 5.2 years ago by user56290 • updated 5.2 years ago by Pierre Lindenbaum100k
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Answer: A: Vcf File With Variants And Genotypes For A "Single Individual"
... I had the same problem. I eventually used Complete Genomics public data set of only 69 genomes. And I used tabix unix program to extract just part of it. A 78GB problem turned into <5 MB file problem. ...
written 5.2 years ago by user56290
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Comment: C: Gc Content In Exome Sequencing And Filtration.
... what is CG? Can you edit your question to fix it. ...
written 5.3 years ago by user56290

Latest awards to user56

Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For Vcf And Copy Number Variations - How These Could Be Displayed?
Supporter 4.3 years ago, voted at least 25 times.
Appreciated 5.2 years ago, created a post with more than 5 votes. For Vcf And Copy Number Variations - How These Could Be Displayed?
Student 5.2 years ago, asked a question with at least 3 up-votes. For Vcf And Copy Number Variations - How These Could Be Displayed?
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Windows-Bases Software Packages Which Can Analyze Vcf Files
Popular Question 5.6 years ago, created a question with more than 1,000 views. For How To Obtain At Least 30 Realistlic Example Vcf Files?

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