User: German.M.Demidov

gravatar for German.M.Demidov
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Tübingen
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Posts by German.M.Demidov

<prev • 425 results • page 1 of 43 • next >
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Genotyping: array variants from WGS
... Dear community members, I need to genotype 6 millions of array markers from a BAM WGS file. It works perfectly for substitutions, e.g., ref allele C, alt allele G,, but indels are problematic - the "format" of array variants is a bit different, for example, ref/alt alleles for array can be: ACG A ...
array wgs written 7 days ago by German.M.Demidov1.9k
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Deviance in allele frequencies between arrays and WGS
... Dear community members, I am trying to adapt a PRS score from arrays ([famous 313 markers breast cancer PRS][2]) to thousands of WGS data. There were 5 array variants which were not found in VCF calls - I found linked variants or fixed the notation. But there are 6-10 other variants where the all ...
array gwas prs wgs written 18 days ago by German.M.Demidov1.9k
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Comment: C: Is it possible to infer tumor purity from tumor-specific Variant Allele Fraction
... Only if your tumor is far from 100% purity (say, 90%). Otherwise it is not really reliable. ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Phylogenetic tree for CNVs
... Better don't mix deletions and duplications at all. These are different events, happened in different evolutionary time. Or, if you want, you may put an exact copy-number instead of 0s and 1s (0,1,2,3,4,5,6 etc) - and calculate Manhattan distance instead of Hamming distance. ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Phylogenetic tree for CNVs
... Hi, yes, it looks as a correct format - but why this CNV chr15:8924153-8982938 0 0 0 0 has only 0s? It mean none of the samples have this CNV. Also - deletion and duplication should be distinguished. The easiest way to calculate a matrix of distances is to use R and the command https: ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Phylogenetic tree for CNVs
... At first, you need to create a table where row names will be distinct CNVs. Then for each sample you may put 1 if this sample has this CNV and 0 if it does not have this CNV. Then you may simply calculate Hamming distance. ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Phylogenetic tree for CNVs
... A phylogenetic tree starts (in the most popular class of methods) with a distance matrix. Once you are able to calculate some sort of distance between 2 samples with CNVs - you're done, you put the matrix of distances into Neighbor-Joining and you have it. Otherwise you need to represent your data ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Help with CNV calling using ExomeDepth
... I used the instruction located under the title "10 How to loop over the multiple samples" from the vignette. It starts from "data(Conrad.hg19)" (which means - load this data based on hg19) and it continues to use this data. If you are able to modify files and execute the first 2 commands from the se ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: Help with CNV calling using ExomeDepth
... Hi, the biggest problem will be to switch to HG38. This is not a trivial replacement here, I think - too many annotations there are based on hg38. ExomeDepth is a good tool, but for a beginner who wants to work with HG38 I'd suggest to try some other tool. ...
written 7 weeks ago by German.M.Demidov1.9k
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Comment: C: what is the meaning of "consensus mutation"?
... I absolutely agree with you, even though I am a part of this problem ...
written 8 weeks ago by German.M.Demidov1.9k

Latest awards to German.M.Demidov

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Inconsistent Coverage on X chromosome between genders
Popular Question 3 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Popular Question 9 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
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Popular Question 11 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 12 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
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Scholar 14 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Scholar 15 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Appreciated 15 months ago, created a post with more than 5 votes. For ClinCNV: CNV detection from short reads
Scholar 15 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Student 16 months ago, asked a question with at least 3 up-votes. For Ploidy Correction In NGS cancer data (human)
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 3.2 years ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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