Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
what is DP4 in VCF (Variant Call Format) and AF1? gcrdb Bioinformatics 8 01-20-2015 09:37 AM
VarScan2 somatic output (genotype call) desmo Bioinformatics 1 12-27-2012 07:49 AM
Help figuring out variant call format (vcf) bmtb Bioinformatics 1 12-11-2012 12:09 AM
VCF file format QUAL column ddaneels Bioinformatics 0 05-22-2012 05:44 AM
An example, multi-sample VCF file? dagarfield Bioinformatics 0 10-18-2011 07:20 AM

Thread Tools
Old 04-30-2015, 01:56 PM   #1
Location: Georgia

Join Date: Mar 2013
Posts: 15
Default Varscan2 multi-variant samples VCF output with empty sample call FORMAT column?


I have Varscan2 generated multi-sample (three samples total) variant VCF file.
I ran Varscan2 on default settings.

For few variants, there is no variant call FORMAT string (e.g., "0/1:2:11:." ) for the third sample, it is completely empty; however for the first two samples there is a variant FORMAT string.

Does anyone know what is the reason for an empty FORMAT specific to a sample in Varscan2 output? is it the read depth?

Thank you.

BhariD 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 08:21 PM.

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