Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent

Similar Threads
Thread Thread Starter Forum Replies Last Post
Haplotype frequencies mrw3288 Bioinformatics 7 03-03-2016 05:18 AM
Variant Calling outside Torrent Suite and TVC gmarco Ion Torrent 14 06-09-2014 01:32 AM
dbSNP frequencies JohnK Bioinformatics 2 12-05-2013 09:36 AM

Thread Tools
Old 10-19-2015, 06:21 PM   #1
Junior Member
Location: Japan

Join Date: Jun 2015
Posts: 8
Default 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%?)

upload img


image hosting websites


photo sharing sites

Thank you for your attention, your help is much appreciated.
hanco is offline   Reply With Quote

tvc, variant calling, variant frequencies

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:38 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO