Question: Calling CNVs in exomes - CLAMMS
gravatar for kath.a.fawcett
6 months ago by
kath.a.fawcett0 wrote:


I would like to identify CNVs from a very large exome sequencing dataset (tens of thousands) and the CLAMMS software looks very promising ( Unfortunately, issues raised on GitHub are not responded to and I was wondering whether anyone out there had ever used this software and could help with a naïve question:

The CLAMMS documentation states: "CLAMMS collects seven QC metrics for each sample and performs a fast k-nearest neighbors search algorithm". However, as far as I can tell CLAMMS does not do this automatically as part of the model building or CNV calling steps. Does the user have to generate these QC metrics (using Picard) and identify nearest neighbours themselves based on the example protocol provided?

Thanks very much!


ADD COMMENTlink modified 11 weeks ago by lakhujanivijay5.1k • written 6 months ago by kath.a.fawcett0

Hi kath.a.fawcett

Unfortunately, issues raised on GitHub are not responded

yes, I have also raised several questions in the recent past and none of them were answered. So, IMHO, you should not expect any response from the author about this. I can confirm that CLAMMS does not generate QC as far as the model building and CNV calling part. I can say this confidently because I already have tried that.

Unfortunately, on a separate note, there is something wrong with my reference file because of which I am getting issues.

ADD REPLYlink modified 11 weeks ago • written 5 months ago by lakhujanivijay5.1k
gravatar for lakhujanivijay
11 weeks ago by
lakhujanivijay5.1k wrote:

The supplementary information here says

Query our laboratory information management system to retrieve seven Picard sequencing quality control metrics for each sample: GCDROPOUT, ATDROPOUT, MEANINSERTSIZE, ONBAITVSSELECTED, PCTPFUQREADS, PCTTARGETBASES10X, and PCTTARGETBASES50X

That means, they assume that we calculate that ourselves.

ADD COMMENTlink written 11 weeks ago by lakhujanivijay5.1k
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