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aeeckhou / shallowHRD

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
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where to find the newest shallowHRD_hg38 script? #14

Closed carolinehey closed 10 months ago

carolinehey commented 10 months ago

Apologies for any potential oversight on my part, but where can I find the latest version of the shallowHRD_hg38 script? Or is only the older version available?

aeeckhou commented 10 months ago

Hello,

I have written after I left my previous lab an hg38 version of the script but haven't really tested it thoroughly. I can send it to you by mail but preferably I would advice to align on hg19 and go with the version latest 1.13 available on github just to be safe.

I you want me to send it to you, I am not at my lab currently and don't have the hg38 script on me, I will only be able to send it to you next Tuesday. Tell me if you still want me to send it to you.

Best regards, Alexandre Eeckhoutte

aeeckhou commented 10 months ago

The hg38 script is discussed in another issue here : https://github.com/aeeckhou/shallowHRD/issues/15 . I am closing this issue.

Best, Alexandre