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-   -   Setting Up Variant Frequencies in TVC (http://seqanswers.com/forums/showthread.php?t=63572)

hanco 10-19-2015 05:21 PM

Setting Up Variant Frequencies in TVC
 
Hi everybody,

Currently, I am using Ion PGM Ampliseq Cancer Panel Hotspot v2 and Torrent Variant Caller.
Usually I have only few number of coverage, for example 30 of 200base reads. Sometimes this kind of data will not appear in TVC. I was wondering if the coverage of my data is too low or do I set the stringency too high.

I always set the variant frequency to "somatic" but I am little confused because in the user guide said that for somatic workflows the threshold is set to 4% frequency for SNPs and 20% for indels. But as you can see in the picture, the minimum variant allele is 0.02 (is it equal to 20% or 2%?)

http://s7.postimg.org/i7mutuoob/Advanced_topics.jpg
upload img

Somatic:
http://s28.postimg.org/puivojv25/somatic_2.jpg
image hosting websites

Germline:
http://s7.postimg.org/gh3tsd757/germ_line_2.jpg
photo sharing sites


Thank you for your attention, your help is much appreciated.


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