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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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How to create gc and map reference for mouse? #46

Open yuanzhao0502 opened 5 years ago

yuanzhao0502 commented 5 years ago

I am trying to use ichorCNA to analysis mouse samples. I have some control samples. So I can not use the human reference files such as gc_hg19_500kb.wig and map_hg19_500kb.wig which in the software package. How can I create or where can I find the gc and map reference for mouse?

gavinha commented 5 years ago

Hi @yuanzhao0502

You can find instructions to generate the reference gc and map files here: https://github.com/shahcompbio/hmmcopy_utils

Best, Gavin

mheskett commented 3 years ago

Thanks! @gavinha could you be more specific or include some commands? it would be a great help to just have a little example script where I can plug in my mouse reference files into hmmcopy in the appropriate format for ichor to work

mheskett commented 3 years ago

OK @gavinha i think this is something that should be included. I tried making mouse reference files myself and now im getting tons of errors because you hard coded the human chromosomes in alot of places it seems.