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despite #262
we are still seeing some false inversions in regions of CNV, e.g.:
https://legumeinfo.org/gcv2/gene;lis=phavu.Phvul.003G002400?algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&thr…
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Dear All,
I'm running the code for inferCNV and everything gets generated correctly but in all the heatmaps generated the reference cell heatmap is missing.
The code I'm using for the run i…
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an Objectives Bayes-HMM. It's referenced in the PennCNV article but not really said to be a bad tool. We should look into it.
https://academic.oup.com/nar/article/35/6/2013/1034786/QuantiSNP-an-Obj…
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These functions are used extensively by gsrc and other packages
http://bioconductor.org/packages/release/bioc/html/DNAcopy.html
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We already know about this, but I'm adding it for completeness with the reference
http://genome.cshlp.org/content/17/11/1665.long
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I have been having an issue where the number of cnvs that are present in cnv_data.txt are much smaller than the number created by parse_cnvs.py
When I run parse_cnv.py on my tumor sample I get appr…
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Af1.x CNV releases will be considered complete without DRCs, only including HMM data and coverage calls.
I think the meaning of the pre-release `pre` arg, e.g. `Af1(pre=True)` will correspond to a …
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### Description of feature
Todo
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cvn_facets is in the blacklist on the current master branch: https://github.com/bioconda/bioconda-recipes/blob/6f666fd2c03adf396a0327a27b6ea14dacba0c55/build-fail-blacklist#L684
I am not able to bu…
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Hi,
I am trying to use CLAMMS to make cnv calls to my targeted panel NGS data. All steps went well except the last step with call_cnv. My bam files are mapped to ucsc hg19, so all chromosomes are s…