Hello everyone,
I am trying to exract copynumbers from genome by sequencing (gbs) data of 630 bwa mem ref aligned bamfiles. The reads are single end and about all of them 90 bp long. The genomes are of snapper fish.
My question is, is there any tool out there that can deal with this datatype well? So far I have come across tools designed for wgs and wes data. What would be the right parameters for said tool with this data in mind?
So far I tried; Control-freec and cnvnator, but im not sure what the best parameters would be due to this data type being rarely used in such a manner.
Any insight on this or recommendations are appreciated!