WES Agilent SureSelect Human All Exon V7

Question

[hood821]

Hello,

I received a ~100 samples worth of WES data (paired fastqs) and I was told that it was processed using Agilent SureSelect Human All Exon V7 kit, and used hg19 as a reference. I don't have any other info, like library prep, or the adapter sequences either (I'm assuming they are the universal illumina adapters). I need to process these: trim, align, etc. Then do variant calling and get copy number. I have never analyzed WES data before, so not sure where to start, or what assumptions can be made for the library prep/adapter sequences. I did manage to get the bed file at least from Agilent's SureDesign catalog. Any help would be great, or direction to a current pipeline or command line calls.

Thanks!

[brunobsouzaa]

Assuming that you have the fastq files, you can follow gatk best practices pipeline for variant calling. For CNV call, I would suggest using both cnvkit and ExomeDepth