User: German.M.Demidov

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Posts by German.M.Demidov

<prev • 401 results • page 1 of 41 • next >
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Comment: C: CNAs calling in tumor-normal WGS data
... Sorry guys for answering my own question - https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator I like this tool so far (not an advertisement, it is just well written with only minor problems for running and looks like it does the job) ...
written 5 days ago by German.M.Demidov1.8k
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Comment: C: CNAs calling in tumor-normal WGS data
... Thank you! Yes, maybe I just should PyClone after calling... ...
written 5 days ago by German.M.Demidov1.8k
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CNAs calling in tumor-normal WGS data
... Dear community members, this question was discussed a lot here, but I could not find an answer that satisfied me fully =) I need to call CNAs in tumor-normal WGS data (only 1 patient, 2 samples). I need to understand sub-clonal structure, purity and ploidy. **ASCAT** - does not like sub-clonality ...
cna tumor-normal wgs written 6 days ago by German.M.Demidov1.8k • updated 5 days ago by non-bot30
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Answer: C: How to astimate the copy number of sex chromosome using QDNAseq or other tools (
... If you just need the number of copies of the whole chromosome, simply count the number of reads on chrX and divide by the number of reads on autosomes. You will have distinct clusters of copy numbers. ClinCNV not only takes into account the sex of the sample, it handles pseudoautosomal regions too ...
written 22 days ago by German.M.Demidov1.8k
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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 11 weeks 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 12 weeks 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 12 weeks 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 12 weeks 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 weeks 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 12 weeks ago by German.M.Demidov1.8k

Latest awards to German.M.Demidov

Popular Question 4 weeks ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Popular Question 7 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Voter 7 months ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 9 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Guru 10 months ago, received more than 100 upvotes.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 11 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Supporter 11 months ago, voted at least 25 times.
Centurion 11 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Appreciated 12 months ago, created a post with more than 5 votes. For ClinCNV: CNV detection from short reads
Scholar 12 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Student 13 months ago, asked a question with at least 3 up-votes. For Ploidy Correction In NGS cancer data (human)
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 2.9 years ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders

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