cnv_facets.R: convenient command line interface for facets

dariober commented 5 years ago

Hi Venkat and All- I'd like to bring to your attention the project cnv_facets that I've been working on recently.

This is a wrapper designed to call CNVs using the facets package via a convenient command line interface:

cnv_facets.R -t tumour.bam -n normal.bam -vcf snps.vcf.gz -o my_cnv

cnv_facets.R takes in input either BAM files, as above, or a pileup matrix created by snp-pileup or a by a previous run of cnv_facets.R.

cnv_facets.R adds some goodies to the functionaliites already in facets:

VCF output with (most of) the metrics from facets
The generation of the pileup file is parallelised across chromsomes for speed (and incidentally fixes issue #101)
The nbhd.snp is optionally automatically computed using the libraries' insert size
--targets option can be used for targeted/WEX sequencing to restrict to regions of interest
There is some basic annotation functionality
Produce histrograms of read depth before and after filtering in addition to the CNV profile and spider plot from facets.

Most of the options available to snp-pileup and facets are available through cnv_facets.R (see cnv_facets.R -h) and it should be straightforward to add the missing ones if required.

For routine work, I find cnv_facets.R more convenient than the low-level facets functions.

Please let me know of any comment, questions, bugs...

veseshan commented 5 years ago

Thanks Dario. Will try it out.

dariober commented 5 years ago

Cool. Let me know if you are happy with the way facets is referenced. FYI, I also posted it here https://www.biostars.org/p/353931/

veseshan commented 5 years ago

The citation is good. Thanks.

apastore commented 5 years ago

Hi Dario, would be possible for you to make a bioconda Package? This would be really help !

dariober commented 5 years ago

@apastore - Thanks for your interest. I thought about making it a bioconda package indeed but since I don't use bioconda myself I left this idea behind. Since you ask I'll have a look though... I would suggest trying the installation route that comes with the package as bash setup.sh ....

(BTW, this sort of questions maybe better issued to https://github.com/wwcrc/cnv_facets)

dariober commented 5 years ago

@apastore - cnv_facets is now on bioconda

apastore commented 5 years ago

Thanks! Much appreciated !

On Dec 20, 2018, at 4:52 PM, Dario Beraldi notifications@github.com wrote:

@apastore https://github.com/apastore - cnv_facets is now on bioconda https://bioconda.github.io/recipes/cnv_facets/README.html — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mskcc/facets/issues/107#issuecomment-449147230, or mute the thread https://github.com/notifications/unsubscribe-auth/AGOdNm9dQBIwMKpeLmS9tS-engkFD6-vks5u7AargaJpZM4ZLmkw.

zhujiaqi2014 commented 5 years ago

@apastore - _cnvfacets is now on bioconda

nice work!

mskcc / facets

cnv_facets.R: convenient command line interface for facets #107