I am new to CNV and a beginner with R language. I am trying to call germline CNVs using exome data using ExomeDepth. I have tried the example given in this it was confusing for when i tried to apply/try with my data. Can someone please help me? explain/show steps which i need to follow to call CNVs. Also in the offical vignette they used Hg19 and i have data using Hg38, how do i go about it?
What data i have?
I have downloaded exome data from 1000g project, cleaned, duplicate marked and BQSR using GATK4 best practices for control. And similarly for sample bam files. In total i have 10 control and 20 sample bam files.
What am i trying to achieve? I am trying to call good quality CNVs using read depth method after read/searching i have finalied Exomedepth.
Since i am a beginner R i am find it difficult, can someone guide me with steps/commads?
Thank you so much for your time.