Question: QC tool for targeted gene panel (like FastQC for WGS)
1
gravatar for nbhardwaj
3.5 years ago by
nbhardwaj130
United States
nbhardwaj130 wrote:

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!

qc targeted-gene panel • 1.7k views
ADD COMMENTlink modified 3.5 years ago by Charles Warden7.2k • written 3.5 years ago by nbhardwaj130

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

ADD REPLYlink written 3.5 years ago by Dan D6.8k

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

ADD REPLYlink written 3.5 years ago by nbhardwaj130

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

ADD REPLYlink written 3.5 years ago by Dan D6.8k
3
gravatar for Charles Warden
3.5 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

Check out CollectHsMetrics in Picard

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

ADD COMMENTlink written 3.5 years ago by Charles Warden7.2k

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!

ADD REPLYlink written 3.5 years ago by nbhardwaj130
1

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.

ADD REPLYlink written 3.5 years ago by Charles Warden7.2k
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