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**Version info**
- bcbio version (`bcbio_nextgen.py --version`):
1.2.3
- OS name and version (`lsb_release -ds`):
CentOS release 6.9 (Final)
**To Reproduce**
```
bcbio_nextgen.py -n 16 sample…
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Today, in order to correctly assign the allelic ratios (and assign colors in the SNP diagrams created with a hapmap) the user needs to provide the correct baseline ploidy. This tells Ymap which possib…
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Xiaotao,
This looks like an amazing tool and I would love to give a shot on our newer Hi-C protocol that uses DdeI and DpnII.
I know your code can work with Arima, so is there something you or I can…
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I want to know how to get the third parameter "df_allele" when running numbat::run_numbat() function.
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thank you so much for this great work!!!
could you please provide more train datasets about ovarian cancer ?
i am so pleased that you would reply to this messages
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Hi,
I am really struggling with convector. I try to launch pipeline.py but results me in some errors so I tried a step by step procedure. I have a folder of BAM files and a .bed file correctly format…
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Does your package help with this type of data?
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Hi,
I've managed to use your package successfully with some suggested tweaks in #74; thank you very much!
I'm getting CNLoH for a very commonly deleted region in my samples and the deletion is con…
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Hi thanks for creating this tool, I have the problem that the input file processed by process_fragment_file.py and the references either provided by you and also the ones created with your "generateRe…
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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …