Moderator: dariober

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dariober9.7k
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Posts by dariober

<prev • 827 results • page 1 of 83 • next >
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Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
... I'd like to bring to your attention [cnv_facets](https://github.com/wwcrc/cnv_facets), a command line tool for detecting copy number variant (CNV), based on the [facets][1] package (*Shen R and Seshan VE, Nucleic Acid Res, [2016][2]*). Recently I've been using the facets package for detecting CNVs ...
tool cancer somatic command line facets cnv written 3 days ago by dariober9.7k
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Comment: C: How to get a matrix gene weights in NMF
... Hi- looking at the documentation of `nmf` (i.e. `?nmf`), it appears the parameter `method` accept a keyword for the distance algorithm. Look at the *Algorithm* section of the docs for the available ones. E.g. `nmf(x, 2, method= 'lee')` ...
written 3 days ago by dariober9.7k
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Answer: A: Link for pre-indexed BWA indices for human reference
... Here? ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ In most cases, the recommended reference is the *_no_alt_plus_* (based on this post by [Heng Lee][1]) [1]: https://lh3.github.io/2017/11/13/which-human-reference-genome-t ...
written 14 days ago by dariober9.7k
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Answer: A: Why NMF for mutation signature analysis
... Sort of complementing @Minstein's answer, there is a nice visual comparison of NMF, PCA and k-means clustering in figure 14.33 (page 555 and paragraphs around it) of [Elements of Statistical Learning][1] (pdf is freely available). You should be able to transpose the message to more bioinformatics qu ...
written 4 weeks ago by dariober9.7k
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Comment: C: Filter VCF with bash commands
... Sorry to be a pain... This fails if the QD tag is the first one in the INFO field since in such case it will not be preceded by `;`. ...
written 5 weeks ago by dariober9.7k
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Comment: C: Filter VCF with bash commands
... Just a couple of notes, if I'm not mistaken... the perl script will not interpret correctly tags ending in `QD`, e.g. a line with `XQD=10;QD=2` will be incorrectly returned. Also, negative numbers are not parsed correctly. If you filter for QD > -10, a line with `QD=-1` will be missed. ...
written 5 weeks ago by dariober9.7k
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Answer: A: Filter VCF with bash commands
... If you want a pure `awk` solution, what about this? awk -v FS="\t" '{ qd=$8; sub(/(.*;QD=)|(QD=)/, "", qd); sub(/;.*/, "", qd); qd= qd+0; if($1 ~ "^#" || qd > 8) { print $0 } }' $FILE However, I would go for `bcftools view` ...
written 5 weeks ago by dariober9.7k
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Comment: C: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
... Granted that I haven't tried nextflow at all... > I prefer [nextflow] because there is no 'final' target I like the idea of a final target since it makes explicit what the pipeline is going to produce. > The workflow [of nextflow] is evaluated at runtime after each step I would say this is ...
written 6 weeks ago by dariober9.7k
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Comment: C: How can i increase variants accuracy?
... Hi Kevin- I'm also interested and puzzled by the idea of subsampling > the odds are shifted in favour of detecting a variant in at least one of the sub BAMs. Sure, but this should come at the expense of increasing false positives, isn't it? Even more extreme, one would call a variant wherever ...
written 7 weeks ago by dariober9.7k
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Answer: A: How to add help function in a snakemake file
... One option may be to print the help when a given configuration key is given, for example `help`: snakemake --config help=1 -s snakefile.smk Help for this script USAGE snamekemake -s snakefile.smk ... I think this works nicely but it's a bit ugly to invoke help using ...
written 7 weeks ago by dariober9.7k

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Appreciated 2 days ago, created a post with more than 5 votes. For A: Output the color code according to number
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Scholar 29 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
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Scholar 12 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file

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