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Old 10-19-2015, 02:22 AM   #5
Junior Member
Location: Japan

Join Date: Jun 2015
Posts: 8

Yes, actually my question relates to variant calling.

I am using Ion PGM Ampliseq Cancer Panel Hotspot v2 and Torrent Variant Caller.
Usually I have only few number of coverage, like I mentioned before, 30 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%?).

I am sorry if my questions is out of the original topic.
Your help is much appreciated, thank you.
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