Picard Bait And Target Sequences For Hybrid Selection Metrics

Question

[Dan D]

I have some human exome sequencing data that was obtained using an Agilent SureSelect 50 mb kit. The sequencing was performed on an Illumina HiSeq.

I am trying to obtain some QC metrics for these data, and after some research it's apparent that Picard Hybrid Selection Metrics is an appropriate tool. However, after searching the literature and doing various google searches, I'm still having trouble distinguishing between bait and target sequences, and how to use them in this particular instance.

I have obtained the BED file for the Agilent SureSelect kit from their earray service. I'm guessing that's my bait sequence, correct? But now I'm wondering how to obtain the target sequence. Is it just the human reference exome from UCSC?

Answer 1

[Sean Davis]

The targets are whatever you would like. More specifically, the targets should include what you think is relevant biologically. The CCDS collection, UCSC genes, refseq, Ensembl/GENCODE are all viable options.

[Dan D]

Great, thanks! I'm glad it's as simple as that. Guess I was over-thinking it.