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I am currently running vcf2circos on a conda environment; installed from https://anaconda.org/bioconda/vcf2circos.
The data is run through GATK pre-processing and then using Manta as a variant caller…
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I am trying to follow the vignette using the set.threshold command and get the following error:
set.threshold(data.original.scan,method="M.eff",level=0.05)
Error in cor(data@geno[, ix]) :
supply…
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Sorry to bother you again, after using the ONT data to call the structure variation, we modified the VCF content with format_add_ALTseq_LR.R. The following error occurred, so we checked the VCF file, …
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## Description
As a developer, I'd like to know what the user's VCF file version is to get us started on what parsing a VCF file into a data structure entails.
The VCF version can be found within th…
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There are various situations where we want to be able to build tiledbvcf-py against an existing external `libtiledbvcf.so`:
* In the conda recipes, we build a separate conda binary for libtiledbvcf…
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Hi developers of `longphase`,
Recently I use `longphase` to phase the ONT sequenced patient data. The phased result looks good but I want to convert the phased VCF to two seperate fasta (one for m…
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Hi,
We are working on incorporating the readVcf function into our Shiny app, but it appears that Shiny is having trouble recognizing the object format.
After completing the upload, we received a…
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Hi eveyone,
I want to verify the best donor numbers of my vcf-data,which is the outputs of cellsnp-lite. I tried the demo command developers provided as follows:
`cell_vcf = vireoSNP.load_VCF('ba…
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I get the vcf file form cnv_facets
I use the WGS data
I wonder How can I get the segment data from the vcf data
especially the column of number of probe
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### Description of feature
I have data consisting of several unrelated trios and several individuals. Is it possible to run the pipeline with just one samplesheet (where cases have different case_id)…