Moderator: dariober
dariober ♦ 9.7k
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Posts by dariober
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... 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 ...
written 3 days ago by
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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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
dariober ♦ 9.7k
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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
dariober ♦ 9.7k
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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
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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... 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
dariober ♦ 9.7k
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