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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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Making a mask for T2T-CHM13v2.0 ? #222

Open mpiersonsmela opened 3 months ago

mpiersonsmela commented 3 months ago

We are using the T2T-CHM13v2.0 reference genome assembly, but we noticed that there is no option to use a mask for this (unlike hg38). Would it be possible to create a mask for this genome assembly?

arpanda commented 3 months ago

Yes, it's possible to add a mask file. Below is the command to create a mask file. The input mask file should be in the same format as the 1000 Genomes Project's strict mask.

> cnvpytor -root MGSCv37_mask_file.pytor -mask ~/hg19/mouse.strict_mask.whole_genome.fasta.gz -make_mask_file

Once you have created the mask pytor file, it can be added to the reference configuration.

For details please check: https://github.com/abyzovlab/CNVpytor/blob/master/examples/AddReferenceGenome.md

As of now, I'm not aware of any publicly available mask file for the T2T-CHM13v2.0 reference genome assembly in the 1000 Genomes Project mask file format. If you know, please share, I can add it with CNVpytor.

Thank you, Arijit

mpiersonsmela commented 3 months ago

Thanks, I'll give it a try! And I'll let you know if I can find a mask file.