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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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how to start Somatic-WGS? UpdateEnvironmentMono is where #103

Open worker000000 opened 5 years ago

worker000000 commented 5 years ago

Dear author, I do not know how to find UpdateEnvironmentMono ?can you help me? how to run these two steps image

eroller commented 5 years ago

That appears to be some outdated documentation. Newer versions of Canvas run using dotnet core. The README has an example command line:

dotnet /CanvasDIR/Canvas.dll SmallPedigree-WGS --bam=/basespace/Projects/canvas/AppResults/bams/Files/father.bam --bam=/basespace/Projects/canvas/AppResults/bams/Files/mother.bam --bam=/basespace/Projects/canvas/AppResults/bams/Files/child1.bam --mother=mother --father=father --proband=child1 -r /basespace/Projects/canvas/AppResults/canvasdata/Files/kmer.fa -g /basespace/Projects/canvas/AppResults/canvasdata/Files/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta --sample-b-allele-vcf /basespace/Projects/canvas/AppResults/snvvcf/Files/Pedigree.vcf.gz -f /basespace/Projects/canvas/AppResults/canvasdata/Files/filter13.bed -o /tmp/gHapMixDemo --ploidy-vcf="/basespace/Projects/canvas/AppResults/snvvcf/Files/MultiSamplePloidy.vcf"

worker000000 commented 5 years ago

canvas has five mode, is it ok to call cnv by just one tumor sample, without control or PoN,

Somatic-Enrichment - CNV calling of a somatic sample from targeted sequencing data Somatic-WGS - CNV calling of a somatic sample from whole genome sequencing data

is these two methods suitable for this, if ok, how to exclude germline cnv

worker000000 commented 5 years ago

is there a more detailed instruction for canvas use, I read the supplementary in cancas paper. thanks a lot.

worker000000 commented 5 years ago

That appears to be some outdated documentation. Newer versions of Canvas run using dotnet core. The README has an example command line:

dotnet /CanvasDIR/Canvas.dll SmallPedigree-WGS --bam=/basespace/Projects/canvas/AppResults/bams/Files/father.bam --bam=/basespace/Projects/canvas/AppResults/bams/Files/mother.bam --bam=/basespace/Projects/canvas/AppResults/bams/Files/child1.bam --mother=mother --father=father --proband=child1 -r /basespace/Projects/canvas/AppResults/canvasdata/Files/kmer.fa -g /basespace/Projects/canvas/AppResults/canvasdata/Files/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta --sample-b-allele-vcf /basespace/Projects/canvas/AppResults/snvvcf/Files/Pedigree.vcf.gz -f /basespace/Projects/canvas/AppResults/canvasdata/Files/filter13.bed -o /tmp/gHapMixDemo --ploidy-vcf="/basespace/Projects/canvas/AppResults/snvvcf/Files/MultiSamplePloidy.vcf"

dear author, is there a clear description about canvas five mode of each parameter, the readme just show one mode and no clear parameter explanation, thanks a lot.

worker000000 commented 5 years ago

there si only SPW in the wiki, it is really hard for us to use this wonderful tool, the urgent thing is to give some tutorials as soon as possible. thanks a lot.

eroller commented 5 years ago

The best place to find a description of the algorithm is https://github.com/Illumina/canvas/blob/master/SoftwareDesignDescription.pdf

For usage info the best place to start is the command line help information. Use --help with any of the modes for a full set of options and description. For more detailed information you can search issues here or ask a new question.

Somatic-WGS and SmallPedigree-WGS are the only workflows that have received any updates over the last year. Germline-WGS has been deprecated in favor of SmallPedigree-WGS. The Enrichment modes are not working in versions after 1.11.

There is also a book chapter containing more detailed usage information for Canvas if you are interested in picking it up. Springer Protocols, Copy Number Variants Methods and Protocols Derek M. Bickhart Editor. Canvas is chapter 12.

worker000000 commented 5 years ago

you mean the two enrichment mode are not working any more and germline-WGS has been deprecated, so canvas can use just Somatic-WGS and SmallPedigree-WGS - CNV, just these two modes, am I right? thanks a lot. image

eroller commented 5 years ago

In the latest version, that is correct. Only Somatic-WGS and SmallPedigree-WGS should be used. If you need the enrichment workflows you will need to use 1.11 which runs under mono and not dotnet

worker000000 commented 5 years ago

thank for your reply, can i ask why in the latest version, why you drop the three in dotnet. I think canvas is really powerful, a better docs should be here if you are free.

eroller commented 5 years ago

Germline-WGS is single sample only. SmallPedigree-WGS supports single and multi-sample so Germline-WGS is redundant.

We stopped supporting/testing the Enrichment workflows so they have various bugs in newer releases.

worker000000 commented 5 years ago

you said only Somatic-WGS retained, which just fit for one sample only of WGS, so canvas does not support for targeted sequence any more? since you just use one sample, how you drop the normal variant(germline variant), thanks a lot.

eroller commented 5 years ago

Correct, the latest versions of Canvas do not support targeted sequencing. In fact, there are no plans for new Canvas releases. Going forward we are focusing on improving the DRAGEN CNV caller, which will perform equally well to Canvas and have the benefit of faster analysis time.

The Somatic-WGS does not drop normal variants. Normal variants, if still present in the tumor sample, will be called by the Somatic-WGS workflow. You can separately perform SmallPedigree-WGS analysis of the normal sample and cross-reference the call sets to see which normal sample variants are still present in the tumor sample.

worker000000 commented 5 years ago

DRAGEN CNV caller, is this free? thanks for you kind and professional help

eroller commented 5 years ago

you mean open source? not at the moment, but I believe there are longer term plans to make it open source.

worker000000 commented 5 years ago

thanks for people like you making the world better