SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bbmap callvariants.sh multisample vcf format, wrong number of fields Greg Bioinformatics 5 04-25-2018 12:00 AM
yet another question regarding vcf format mstagliamonte Bioinformatics 4 07-19-2016 12:53 PM
Question: NGS SNP data - trouble recomputing INFO values in VCF SMusker Bioinformatics 0 02-09-2016 11:56 PM
Samtools mpileup vcf format question k2bhide Bioinformatics 1 02-25-2011 09:54 PM
VCF format question NGS2009 Bioinformatics 1 02-14-2011 05:07 AM

Reply
 
Thread Tools
Old 09-24-2019, 12:01 AM   #1
lollysticky
Junior Member
 
Location: Flanders, Gent

Join Date: Aug 2010
Posts: 4
Default VCF question regarding missing INFO or FORMAT fields

A combination of two questions which I can't directly resolve from reading the v4.3 specifications. They're mostly hypothetical as most variants won't encounter this situation


Question 1
If there is no INFO information (so: column 8 in the VCF file) present for a given variant, is the column just empty or is it represented by '.' ? Not every variant needs to have the same INFO fields present, so this scenario seems plausible.

Question 2
If There is no FORMAT/GENOTYPE information (so: column 9 and 10 in the VCF file) present for a given variant, are both columns empty or represented by '.' ? Same as above: not every variant needs to have the same FORMAT fields present, so this scenario seems plausible.
lollysticky is offline   Reply With Quote
Reply

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 12:07 AM.


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