Question: Mutational Calling with SomaticSeq
0
gravatar for morovatunc
3.2 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

 

Dear all hi,

I would like to know if you guys could help me about starting calling somatic mutations with somaticseq. Right now I am overwhelmed with the data and the program thats why I cannot produce data.

My biggest problem is I am not sure how can I create a new classifier. Should I use the data that was studied in the paper as a ground truth? or directly start off new with my current data. 

As I understand from the manual, I have to call mutations with individual programs first. After that I will combine the outputs of the individual callers by somaticseq to create a classifier. Then call mutations with somaticseq algoritm? Once I created this classifier, I dont have to redo the creating classifier part. I have to only call the mutation with created classifier.

I will be working with the data from ICGC and TGCA thats why I have to create a robust pipeline. Since my data is too big, I am confused about the part where I create my classifier. How can I build a classifier which will give me true results for my data which is consisted of +250 samples including tumor and normal pairs? 

Any information will be valuable for me. If there is someone who has used this program before PLEASE HELP ME !!!

Thank you,

Tunc

somatic mutations ngs • 909 views
ADD COMMENTlink modified 2.9 years ago by ttom200 • written 3.2 years ago by morovatunc400
1
gravatar for ttom
2.9 years ago by
ttom200
ttom200 wrote:

I had similar questions and these are the information I received from the developer

"SomaticSeq published classifier we put up on gDrive is trained based on Stage 3 of the DREAM Challenge, with the 5-tool classification for SNV (i.e., Mutect, Varscan, JointSNVMix, SomaticSniper, and VarDict) and 3-tool classification for INDEL (Indelocator, Varscan, and Vardict). If your call set did not use those tools, then the classifier is invalid. For the tools that you did you use, it is going to assume that the tools classified them as false positives. If you want to train your own classifier, just make sure the training set and the testing set used the same parameters for all the tools, etc."

You can always check contact them for more details "Fang, Li Tai [li_tai.fang@bina.roche.com]"

ADD COMMENTlink written 2.9 years ago by ttom200
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