Question: Confusion with Varscan somatic filters
gravatar for mkaushal
5.5 years ago by
United States
mkaushal110 wrote:


I am running Varscan somatic to identify somatic mutations in normal tumor samples. These are the filters I am using:

--min-coverage 25 --min-avg-qual 30  --min-var-freq  0.05 --somatic-p-value 0.05 --normal-purity 1
--tumor-purity 0.5 --min-reads2 3

Please note though I have used --min-var-freq  of 0.05 , I am still getting variants with vaf < 5%. Example:

chr1    762273  .       G       A       .       PASS    DP=284;SOMATIC;SS=2;SSC=13;GPV=1E0;SPV=4.0376E-2        GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:156:152:0:0%:37,115,0,0   0/1:.:128:121:4:3.2%:27,94,1,3

Can someone please help me understand what I am missing here. Is this because of some other filter I am using? Or did I get the usage of --min-var-freq wrong?




somatic filters varscan • 2.7k views
ADD COMMENTlink modified 5.4 years ago by sergio.lois0 • written 5.5 years ago by mkaushal110
gravatar for sergio.lois
5.4 years ago by
sergio.lois0 wrote:

Hi Madhurima,

Last days I have been playing with this parameters and I think that this situation is possible because you are considering a tumor purity of 0.5. In this scenario:

min-var-freq = min-var-freq x tumor-purity

So, the new cut-off for variant allelic frequency is 2.5% (0.05 x 0.5).  Is it possible?

Thanks for sharing it!


ADD COMMENTlink written 5.4 years ago by sergio.lois0

Hi Madhurima and mbhattacharjee,

Could you please explain what filtering criteria you used for called snv from varscan2. I tried to use two of the scripts from varscan, with very little overlap between them. I have posted my quesion here, Varscan Filtering scripts: very little overlap between output of varscan filtering scripts

Thanks in advance.


ADD REPLYlink written 5.3 years ago by Chirag Nepal2.2k
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