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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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rds files compatibility #66

Open CuriusScientist opened 4 years ago

CuriusScientist commented 4 years ago

Hi! what I have understood from going through the ichorCNA commands is that window size for --gcWig, --mapWig and --normalPanel should be same, for instance, 1000 kb.

I am using files mapped to hg38 and want to try window size lower than 500 kb but the .rds files are only present for 1mb and 500 kb. Will it be possible for you to provide .rds files for 50 kb and 10 kb or there is any other way to get over this issue?

gavinha commented 4 years ago

Hi @CuriusScientist

Are you referring to additional bin sizes for the normal panel? We provide the gc and map wig files for 50kb and 10kb so you could ignore the panel for these sizes. I do recommend that if you use these smaller bin sizes, you should also try to use a matched normal sample. The snakemake pipeline here doesn't support matched normals, but (TitanCNA)[https://github.com/gavinha/TitanCNA] does. Since you are using this small bin sizes, I assume the sequencing coverage of your samples is higher so it might be worth looking into Titan.

Hope this helps. Gavin

CuriusScientist commented 4 years ago

Dear @gavinha

Yes, I was referring to additional bin sizes for the normal panel.

If I understood you correctly then for smaller bin sizes, which can be only used for data with higher sequencing coverage, instead of the normal panel, I should use the matched normal sample.

Also, ichorCNA does not have an option for a matched normal sample. Is --NORMWIG from ichorCNA, not the option to have matched normal sample?

I will surely look into TitanCNA.

Thanks, Nitin Sharma