search

mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
24 stars 9 forks source link

How to calculate the fraction of the exome in ROH #12

Closed salonso65 closed 2 years ago

salonso65 commented 2 years ago

Hi! I was thinking about how to calculate which percentage of an exome that the total sum of ROH represents (to try to estimate some kind of inbreeding coefficient). My problem is how to estimate the total length of the exome in question according to AutoMap for each sample, and how this depends on teh parametres selected.

Any help?

Thanks in advance

mquinodo commented 2 years ago

Hi, I apologise for the late answer. I think it is reasonable to use the size a the full genome without N-bases. For hg19 it is 2,897Mb. Best, Mathieu

salonso65 commented 2 years ago

ok, thanks a lot!

santos

From: Mathieu Quinodoz Sent: Monday, May 9, 2022 4:15 PM To: mquinodo/AutoMap Cc: salonso65 ; Author Subject: Re: [mquinodo/AutoMap] How to calculate the fraction of the exome in ROH (Issue #12)

Hi, I apologise for the late answer. I think it is reasonable to use the size a the full genome without N-bases. For hg19 it is 2,897Mb. Best, Mathieu

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>