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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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Creation of Mappability Files #29

Closed mej54 closed 5 years ago

mej54 commented 6 years ago

Hi,

I'm wondering how the mappability wig files under inst/extdata were created? I'm hoping to create these files with 1kb windows.

Thanks in advance!

gavinha commented 6 years ago

Hi @mej54

The instructions to create the GC content and mappability files are provided https://github.com/shahcompbio/hmmcopy_utils

For hg38, Bowtie doesn't work when trying to create mappability score files. Others have been using gem-mappability tool for this. I have recently added mappability (and GC) files for other bin sizes. I can also include on for 1kb.

Best, Gavin

gavinha commented 5 years ago

This issue is resolved in #22