User: markus.riester

gravatar for markus.riester
Reputation:
230
Status:
Trusted
Location:
Scholar ID:
Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
1 year, 1 month ago
Email:
m*************@gmail.com

Posts by markus.riester

<prev • 26 results • page 1 of 3 • next >
1
vote
2
answers
144
views
2
answers
Answer: A: Infer somatic mutations without normal control
... 1. I assume you are talking about high coverage data? Then yes, ad hoc, but pretty standard. Ideally one examines the coverage of the assay over many samples and understands why some regions have low coverage. Then understand how this impacts your variant calling. 2. Should be fine. 3. Depends w ...
written 8 days ago by markus.riester230
0
votes
1
answer
128
views
1
answers
Answer: A: WES chromosome Y off-target reads coverage compare to autosome
... Should be much lower because of the very low mappability of chrY. If you have WES, then why using off-target reads? For most kits, you will have plenty of perfectly mapping exons that will show 0 reads in females (or very few in case of minor cross-sample contamination). ...
written 16 days ago by markus.riester230
1
vote
5
answers
315
views
5
answers
Answer: A: Suggestions regarding bioinformatics journal
... If the critique of reviewer 3 has absolutely no merit, I would consider an appeal. It was probably a very tough decision for the editor as well, so he might be willing to hear your case again. Be nice, admit the flaws in presentation etc. 8 months until rejection is a worst case scenario, but stil ...
written 4 weeks ago by markus.riester230
0
votes
1
answer
297
views
1
answers
Answer: A: ABSOLUTE R package - CreateReviewObject Error, Error in seq_len(M) : argument mu
... I cannot comment on the crash, but I recommend reading the [ABSOLUTE][1], [ASCAT][2] and more recent papers like [Sequenza][3]. Running ABSOLUTE with only segmented data is pretty much futile. You need germline allelic fractions to determine the number of maternal and paternal copy numbers, which ar ...
written 3 months ago by markus.riester230
0
votes
2
answers
386
views
2
answers
Comment: C: Tumor purity estimation by allele frequency of COSMIC identified somatic mutatio
... Partly because they don't adjust for purity and copy number, as they state in the Discussion. With normal contamination, there are ways to discriminate somatic from germline. At least there are ways to calculate those probabilities accurately. ...
written 4 months ago by markus.riester230
2
votes
1
answer
272
views
1
answers
Answer: A: CNV calls in VCF format, conversion to PCAWG-11 Calibration
... - Yes, "pos" should be start. - "major_cn" is total copy number - minor_cn (major+minor=total, minor <= major) - cellular_prevelance is the fraction of tumor cells with this alteration. Looks like your tool does not report this value. You can set to 1. There are a gazillion VCF parsers and li ...
written 4 months ago by markus.riester230
0
votes
0
answers
553
views
0
answers
Comment: C: tumor only variant calling tools
... That is exactly implemented in https://doi.org/10.1186/s13029-016-0060-z (https://bioconductor.org/packages/devel/bioc/html/PureCN.html). For targeted panels, this will only work if you have sufficiently large pool of normals, even coverage and either hybrid capture data (gives you off-target read ...
written 4 months ago by markus.riester230
0
votes
0
answers
553
views
0
answers
Comment: C: tumor only variant calling tools
... Depends. Most clinical FFPE samples have low purity (typically well <75%) and high coverage. Their SGZ algorithm (cited in https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2) then adjusts allelic fractions for purity, ploidy and local copy number. Our PureCN is fairly s ...
written 4 months ago by markus.riester230
0
votes
1
answer
440
views
1
answers
Answer: A: WES samples failing ABSOLUTE
... Looks like the copy number ratios are not in the expected format and range. Check that ABSOLUTE knows that you are providing total copy number ratios and not allele-specific (HAPSEG) ones, i.e. set copy_num_type argument to "total". Make sure that they are correctly log-transformed. As a general re ...
written 5 months ago by markus.riester230
1
vote
1
answer
322
views
1
answers
Answer: A: Merging CNVs from multiple tumor samples from the same patient
... I think superFreq (https://github.com/ChristofferFlensburg/superFreq) is pretty much the only allele-specific caller designed for multiple samples. In case your data is from whole-genomes, there might be others. The benefit of supporting multiple samples is mostly in tracking cellular fractions of ...
written 5 months ago by markus.riester230

Latest awards to markus.riester

Scholar 4 months ago, created an answer that has been accepted. For A: Somatic variant caller
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 6 months ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 6 months ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 6 months ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 10 months ago, created an answer that has been accepted. For A: Somatic variant caller

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 666 users visited in the last hour