extract copy number variation from read count file of WES

Question

[ghaneianabatm]

Hello, I have 40 excel files (read counts) of WES and i want to extract copy number variations from these. Please introduce me proper tools or guidelines.

[Thind amarinder]

I am not sure, what do you mean by read count in the excel file. But if you are looking for copy number alterations tools, please refer to some studies https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3421-1 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1705-x

You may need bam files for these tools.

[ghaneianabatm]

Thanks a lot for your answering to my question. My intent about read counts is the final file achieved from analysis of fastq file. fastq>SAM>BAM>VCF>Excel (read counts)

[Thind amarinder]

These are .vcf files with annotation of the variants. The next steps depend on your biological question/s. If you want to summarize all of them in one place. Maybe you would like to use openCravat or MAF (R tool) etc. if you explain, what information are you looking for from these .vcf files? I can explain further.