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Hi,
I created a .bed file for a single sample as,
Chr Start End sampleNA-78
chr1 10173 10230 1
chr1 10458 10603 1
chr1 11081 11227 1
chr1 11228 11256 1
chr1 11854 12022 1
chr1 12646 12780 1
c…
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I propose to implement a review and merge process, similar to what we have in https://github.com/operate-first/ and discussed in https://github.com/operate-first/apps/issues/81
This would encompass…
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We could have one byte per variant and file:
* **PASS**: 1 bit coding wether is PASS
* **Type**: 3 bits encoding for SNV, INDEL, INSERTION, DELETION, MNV, CNV, REARR (translocations and inversions…
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The current hierarchy of variant types is pretty simple and flat. We could make it more detailed by adding more levels to it, for instance, an indel may be an insertion or deletion.
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Hello,
thanks for AA! It works class!
I was wondering if I can use my own fasta file (used to generate the bam)?
Maybe you can give a brief explanation about the data_repo folder structure. Should…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Summary
When connecting to a MySQL database, the program may use multiple connections and fail to close them w…
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Hi!
I just wanted to check a few things and get some suggestions on how we do CNV analyses. Currently, we are using CNVKit from SevenBridges. I hope that I can get some better understanding of the …
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Dear pfrofessor,
Thanks a lot fot providing such a powerful tool for cnv.
I found a very strange error,
a same command in cnvkit fails in the first time, but success in the second time. it is a ra…
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Hi raphael group,
Thanks for developing this amazing tool. I am quite new to clonal tree construction and I am learning to use the SCARLET tool. I tried with the following command using the example…
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Change warning message to venn diagram of sample IDs in mutalisk dataset vs MAF dataset