Entering edit mode
5.5 years ago
bioming
•
0
Hi everyone,
Recently, I try to call structural variants from two different population, female and male, of one fish species. And I will try to compare the differences between the two sexes. So I have two questions for this work.
Firstly, As most of these software were built for human genome SV calling, they usually have two model germline and somatic. I think germline model may fit my project. But I am not 100% sure.
Secondly, I have used Delly germline calling SVs for male and female respectively. I am searching some tools to call the differences between the two sexes genotype.bcf file obtained with delly. Anyone has some instructions or suggestions to me!
I hope my answer is clear. And thanks for your attention and response in advance.
Do you have any reason to expect biologically relevant SVs between gender?
And yes, unless you are looking for cancer variants you need the "germline model".
Hi WouterDeCoster, thanks a lot and sorry for later reply. As sex determining gene may derived from duplication of autosome, so we try to compare the two sexes and hope to get some signals of duplication difference between male and female. what makes this analysis more complicated is that we mapped pooled male and pooled female reads to female genome reference. I do not have experience for analyzing SVs, so I just wonder whether these pooled data could suit for this kind of analysis?