QC tool for targeted gene panel (like FastQC for WGS)

Question

[Floydian_slip]

Hi, Just like we have FastQC for QC of WGS and exome-data, is there a tool for QC of targeted-gene panel studies? The reason I ask is because some of the metrics from FastQC such as GC content may not hold for a small region captured in a focused NGS panel.

Thanks!

[Dan D]

Are you still wanting to look only at FASTQ data, or do you want something that QCs post-alignment?

[Floydian_slip]

I was looking for something to analyze FASTQs as well. Would you have a suggestion? For post-alignment, Charles mentioned HsMetrics from Picard below.

[Dan D]

Can you be more specific about what FastQC is lacking that you need?

Answer 1

[Charles Warden]

Check out CollectHsMetrics in Picard

https://broadinstitute.github.io/picard/picard-metric-definitions.html#HsMetrics

[Floydian_slip]

Thanks Charles! One quick question that I could not clarify upon skimming through the description: What is the difference between Bait and Target region? Should they both be input in a .bed format? Thanks again!

[Charles Warden]

They both should be bed files. The baits are the exact position covered by your baits (assuming an array-based pull-down method) and region is the region associated with the baits (probably an exon). If you are using an amplicon-based target design, they will be the same.