Question: Processing Whole Genome Sequencing data (shallow) and call Copy Number Variations
gravatar for Alejandro Jimenez Sanchez
2.7 years ago by
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

Dear all,

We are proposing a project where we want to perform shallow Whole Genome Sequencing (<1x) on DNA obtained from tumour FFPE human samples.

I have worked before with Whole Exome Sequencing and I have called SNVs and so on, but I haven't worked with WGS yet.

Does anyone know of any good tools and steps to get copy number variations from shallow WGS?

I haven't seen any paper that benchmarks tools yet, but if someone knows about this topic and could give some light in this, I would appreciate it very much.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Alejandro Jimenez Sanchez120
gravatar for AlexRT
2.7 years ago by
AlexRT10 wrote:

If it's for germline copy-number variations, the 1000 genomes projects has called structural variations including copy number changes from individuals with ~7X WGS ( You can use GenomeStrip ( or Delly (, or Lumpy (

Since you have really low-depth WGS, the key is to have enough samples to pick up power for detecting variants in carriers vs non-carriers in the population. I never used <1x WGS for copy-number, but it might be harder to detect call copy-neutral variants such as inversions.

ADD COMMENTlink written 2.7 years ago by AlexRT10

It is for copy number variations in tumour tissues, so germline changes would be removed.

ADD REPLYlink written 2.7 years ago by Alejandro Jimenez Sanchez120

Oups forget the comment then.

ADD REPLYlink written 2.7 years ago by AlexRT10
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