User: German.M.Demidov

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Posts by German.M.Demidov

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Answer: C: correlation pearson and spearman PValue
... it can easily happen - e.g. bottom right plot from the quartet https://en.wikipedia.org/wiki/Anscombe%27s_quartet ...
written 9 days ago by German.M.Demidov1.8k
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Comment: C: GermlineCNVCaller- Interval scattering for WES data
... I guess it is used to "smooth" the coverage of each bin using bins right next to the one. So, if the goal is to find one-exon CNVs, this step surely has to be skipped. I wander if the results will look good without that step - please let us know if the calls look fine for you in the end =) It is qu ...
written 11 days ago by German.M.Demidov1.8k
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Comment: C: GermlineCNVCaller- Interval scattering for WES data
... I am not sure if I fully understand what GATK asks to do, but my understanding is that with this binning in WES it either 1) tries to involve off-target coverage, 2) it is not needed. I would not do binning of WES data at all (unless one want to detect intra-exonic variants or it is off-target reads ...
written 11 days ago by German.M.Demidov1.8k
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Comment: C: GermlineCNVCaller- Interval scattering for WES data
... I have worked with GATK caller with tumor-normal mode only - there off-target reads are beneficial, but for germline exome seq I would say it creates just additional complexity without a significant increase in sensitivity (it can detect only large CNVs). Surely 1KB is too small - maybe try 25KB ins ...
written 11 days ago by German.M.Demidov1.8k
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Comment: C: Interpreting paired-end tumor-normal WES
... You don't :) information about which is normal which is tumor is saved separately, not in fastq file. For a sequencing machine there is no difference if one sequence normal or tumor tissue. This is likely either tumor or normal file. ...
written 12 days ago by German.M.Demidov1.8k
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Comment: C: Publicly Available WGS Samples for Panel of Normals?
... Not really, it is a totally different variant caller which we use to call tumor variants with absence of normal matched pair :) but well, then keep up to your plan! ...
written 14 days ago by German.M.Demidov1.8k
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Comment: C: SNPs and DEL/MNP in the same position. (DEL or SNP ??)
... It can be a repetitive region in your bacteria or segmental duplication as well. It may be an assembly problem, not a variant caller problem ...
written 15 days ago by German.M.Demidov1.8k
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Comment: C: SNPs and DEL/MNP in the same position. (DEL or SNP ??)
... Check it in IGV :) as @RamRS explained it is totally fine for diploid organisms ...
written 15 days ago by German.M.Demidov1.8k
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Comment: C: Calculating empirical allele frequency
... Hi, I agree, in this case (as I understood from the description) DP is equal to sum of AD >It says DP=51, but then later GT:AD:DP:GQ:PL 0/1:36,11:47:99:210,0,1046 lists DP=47 and then of curse AD/DP is the right way as well as AD / sum AD ...
written 15 days ago by German.M.Demidov1.8k
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Comment: C: SNPs and DEL/MNP in the same position. (DEL or SNP ??)
... my recommendation remains the same: check 1 variant in 1 sample in IGV and then you'll understand the situation. After that - extrapolate the conclusions for all 1000 samples. ...
written 15 days ago by German.M.Demidov1.8k

Latest awards to German.M.Demidov

Popular Question 4 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Voter 5 months ago, voted more than 100 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 6 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Guru 8 months ago, received more than 100 upvotes.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 8 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Centurion 9 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Appreciated 10 months ago, created a post with more than 5 votes. For ClinCNV: CNV detection from short reads
Scholar 10 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Student 11 months ago, asked a question with at least 3 up-votes. For Ploidy Correction In NGS cancer data (human)
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 2.7 years ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders

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