Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools tview reference sequence rodney Bioinformatics 20 05-02-2016 12:37 AM
samtools tview totalnew Bioinformatics 1 10-17-2011 06:10 PM
Help interpreting samtools tview dnusol Bioinformatics 3 09-05-2011 08:48 PM
samtools tview EmmaB Bioinformatics 4 07-18-2011 02:43 AM
samtools pileup and tview pparg Bioinformatics 5 11-09-2010 01:53 AM

Thread Tools
Old 02-15-2012, 11:30 PM   #1
Senior Member
Location: Spain

Join Date: Jul 2009
Posts: 133
Default help interpreting samtools tview

Hi, I hope someone helps me find out what is going on here. Samtools is giving me a T/G SNP at position chr19:19737915 in two different sampes.

chr19 19737915 . T G 6.2 . DP=55;VDB=0.0784;AF1=0.4999;AC1=1;DP4=4,9,5,0;MQ=55;FQ=8.65;PV4=0.029,0.009,0.0074,1 GT:PLP:SP:GQ 0/1:35,0,216:18:15:36

chr19 19737915 . T G 20 . DP=24;VDB=0.0656;AF1=0.5;AC1=1;DP4=0,2,4,0;MQ=42;FQ=18.9;PV4=0.067,0.011,0,1 GT:PLP:SP:GQ 0/1:50,0,48:6:12:49

Is it the quality too low? I find the alignment rather strange in this region to believe that is actually a true SNP, but seeing that it is happening in two different samples, it makes me wonder.

Attached Images
File Type: jpeg s_1_tview_chr19_19737915.jpeg (128.5 KB, 47 views)
File Type: jpeg s_4_tview_chr19_19737915.jpeg (138.0 KB, 35 views)
dnusol is offline   Reply With Quote

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 07:28 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO