Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
snpEff & snpSIFT variant filtering doc.ramses Bioinformatics 2 10-21-2014 12:29 PM -specifying minimum read depth? Lspoor Bioinformatics 3 05-27-2013 01:20 AM
recommendations needed for filtering the variant file kjaja Bioinformatics 0 12-09-2011 12:47 PM
variant calling kjaja Bioinformatics 1 11-04-2011 07:16 AM broken on Ubuntu 11.10? kz26 Bioinformatics 1 10-24-2011 10:54 AM

Thread Tools
Old 06-07-2011, 12:54 AM   #1
Junior Member
Location: Switzerland

Join Date: Sep 2010
Posts: 4
Default variant filtering

hi all
I would like to know why the variant below is filtered when I use the default parameters with varFilter.
CFA18 1805 . A T 99 . DP=3421;AF1=0.5;CI95=0.5,0.5;DP4=327,962,694,1438;MQ=18;PV4=9.1e-06,0.00032,0.005,2.4e-06 PLP:SP:GT:GQ 255,0,219:805:8:0/1:99 108,0,174:681:19:0/1:99 101,0,163:671:28:0/1:99 213,0,142:1264:12:0/1:99

Thank you very much for your answers
vidhya is offline   Reply With Quote

samtools, variant filtering, vcfutils

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 08:27 PM.

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