How to obtain a GC content file to use in HMMcopy?
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bpitarch • 0
@0afca487
Last seen 8 hours ago
Canada

I have a BAM file and I want to obtain the copy number profile of that file using HMMcopy, but I don't know how to obtain the GC content file required.

HMMcopy • 105 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

The vignette says this:

It should be noted that due to memory and speed considerations, the raw input that feeds in to this package are required to be generated by programs distributed as part of the HMMcopy Suite available at:

Which is admittedly pretty unhelpful, except it does tell you there's a thing that you can use. And googling that term brought me to this github, which seems like the thing?

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It was indeed very confusing that paragraph, but now I can start working. Thank you so much for your help.

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