Question: Confusion with Varscan somatic filters
1
gravatar for mkaushal
5.5 years ago by
mkaushal110
United States
mkaushal110 wrote:

Hello,

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?

Thanks,

Madhurima

 

somatic filters varscan • 2.7k views
ADD COMMENTlink modified 5.4 years ago by sergio.lois0 • written 5.5 years ago by mkaushal110
0
gravatar for sergio.lois
5.4 years ago by
Spain
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!

Sergio

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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