Question: WES or WGS analysis of cancer samples with no matched germline
1
gravatar for Bogdan
11 days ago by
Bogdan260
Palo Alto, CA, USA
Bogdan260 wrote:

Dear all,

although this question has been asked before (~ 2 years ago), if I may ask it again, as I am looking for some updated workflows, strategies, ideas :

"what would be the acceptable pipeline for processing WES or WGS data from primary tumors that do not have matched germlines sequences ?"

many thanks,

-- bogdan

cnv snv wes wgs • 177 views
ADD COMMENTlink modified 11 days ago by markus.riester180 • written 11 days ago by Bogdan260

What is the aim of the analysis?

ADD REPLYlink written 11 days ago by WouterDeCoster20k

Hi Wouter, thanks : we aim to identify the SNV and CNV in the tumor samples (and some of these samples do not have a matched normal sample).

ADD REPLYlink written 11 days ago by Bogdan260
6
gravatar for markus.riester
11 days ago by
markus.riester180 wrote:

MuTect and FreeBayes for SNVs are probably the most used tools for tumor-only analyses. Copy number, if you have some normals, you can try CNVkit, cn.mops (I think) and GATK4beta. If you need purity/ploidy and want to classify variants as germline vs somatic, there isn't much out yet, so we wrote our own tool PureCN (Bioconductor, try the much improved developer version if you like).

ADD COMMENTlink modified 11 days ago • written 11 days ago by markus.riester180

Dear Marcus, thank a lot for your suggestions. Yes, we have been using MUTECT2 and cn.MOPS for detecting SNV and CNV in germline-tumor pairs. However, when we have only a TUMOR sample (with no GERMLINE sequence), may I ask, how would you run MUTECT2 ?

ADD REPLYlink written 11 days ago by Bogdan260

Just run in without the normal BAM. The GATK3 version of MuTect2 doesn't officially support tumor-only analyses, but will do it. For GATK4beta, it's described in the documentation.

ADD REPLYlink written 10 days ago by markus.riester180

Thanks Marcus ! yes, I am still using GATK 3.5, as we started with GATK 3.5 based pipeline a long time ago . If you do not mind, may I ask, what resource do you use for GATK4beta documentation ? thanks !

ADD REPLYlink written 10 days ago by Bogdan260
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