SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
snpEff & snpSIFT variant filtering doc.ramses Bioinformatics 2 10-21-2014 01:29 PM
vcfutils.pl -specifying minimum read depth? Lspoor Bioinformatics 3 05-27-2013 02:20 AM
recommendations needed for filtering the variant file kjaja Bioinformatics 0 12-09-2011 01:47 PM
variant calling kjaja Bioinformatics 1 11-04-2011 08:16 AM
vcfutils.pl broken on Ubuntu 11.10? kz26 Bioinformatics 1 10-24-2011 11:54 AM

Reply
 
Thread Tools
Old 06-07-2011, 01:54 AM   #1
vidhya
Junior Member
 
Location: Switzerland

Join Date: Sep 2010
Posts: 4
Default vcfutils.pl variant filtering

hi all
I would like to know why the variant below is filtered when I use the default parameters with vcfutils.pl 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
vidhya is offline   Reply With Quote
Reply

Tags
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 01:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO