Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
vcftools install on 14.04.3 cmccabe Bioinformatics 6 09-05-2015 09:05 PM
vcfTools depth filter problem JackieBadger Bioinformatics 3 08-14-2013 07:10 AM
how to check integrity/completeness of bwa sai files ? mccullocha Bioinformatics 0 09-04-2012 01:55 AM
vcftools site filter using bedfile info_nowise Bioinformatics 3 04-19-2012 12:56 PM
DGE - filter or not filter masterpiece Bioinformatics 0 07-11-2011 08:55 PM

Thread Tools
Old 07-05-2016, 11:57 AM   #1
Location: Canada

Join Date: May 2016
Posts: 14
Default Filter by completeness with VCFtools


What is the best way to filter for completeness with VCFtools?

Basically, I would like to only keep SNPs that are present in all individuals (or in 80% of all individuals). I have been using --max-missing or --max-missing-count but I am unsure if it is the right way of doing it.

Any thoughts would be greatly appreciated!
AP38 is offline   Reply With Quote
Old 07-05-2016, 10:15 PM   #2
Registered Vendor
Location: Eugene, OR

Join Date: May 2013
Posts: 521

That is what those options are designed to do so I think you have a good solution.
Providing nextRAD genotyping and PacBio sequencing services.
SNPsaurus is offline   Reply With Quote
Old 07-06-2016, 05:12 AM   #3
Location: Canada

Join Date: May 2016
Posts: 14

Thanks, this is something that I wanted to double check - I have never filtered for completeness and wanted to make sure that I am using the appropriate flags.
AP38 is offline   Reply With Quote

completeness, filter, vcftools

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 07:44 AM.

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