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Test example contains aligned 56 chloroplast sequences downloaded from NCBI. There are 60 partitions (genes and concatenated inter gene regions).
Running that calculations hangs around iteration 6000…
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I've been looking at canned elements, initially to add statuses (as described at https://genomearchitect.readthedocs.io/en/latest/CannedElements.html#statuses)
I can add a couple of status values…
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Hi,
I ran into some problems when predicted mutation effect using ExPecto, which are listed as follows:
1) in my input file *.vcf, whether I should restrict mutations within transcriptional regulat…
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from what i can tell, only one of the two genes in a gene fusion is curated in oscar's database. for example, selection of therapy_variant.id = 724 gives:
+--------------------+--------------------…
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Right now it returns variants that are over certain specified frequency thresholds in gnomad. But for pathogenic thresholds we want to do the reverse, returning those less than the threshold. So we ne…
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Hello,
I would like to perform a CNV calling on WGS samples from Maize only on gene's positions. For that, I have created a script using the genes as target and the batch command. However, the fin…
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Check this WS call
http://bioinfoint.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/clinical/phenotype-gene?include=clinvar
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1) Could non-coding exons interfere with the calculation of the $dist, $d variables in LoF.pm lines 257-263? The code is simply looping over exons in the gene (via perl sub get_gerp_weighted_dist), i.…
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http://doi.org/10.1038/537S63a
This perspective paper is relevant for our discussion of how we categorize disease. I think that these difficulties are something that we'll need to recognize in our pa…
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Hello,
I tried using cegwas2-nf and it doesn't even go through the first process.
I tried to find the cause of this issue, but couldn't find it.
I attach the output when running the command `NXF_…