Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
Supplementing WGS variant calls with RNA-Seq chrismit Bioinformatics 2 05-15-2013 12:01 PM
convert CASAVA variant calls to VCF? krish Bioinformatics 0 12-01-2011 08:44 PM
Complete Genomics Variant Calls quicksand21 Bioinformatics 2 10-11-2011 07:21 AM
merging and de-duplicating structural variant calls (bedpe) splaisan Bioinformatics 0 06-27-2011 07:29 AM

Thread Tools
Old 01-22-2015, 08:24 AM   #1
Junior Member
Location: South Central US

Join Date: Aug 2012
Posts: 7
Default Manual Quality Control for Variant Calls

Hello all SEQers,

I am trying to find some documentation or leads on strategies for the manual quality control of variants that have been called in a whole exome sequencing experiment.

The closest I got was in the GATK 'best practices' summary which basically tells you to check if the variants 'look good'. Obviously this leaves a lot of room for interpretation, but this is the closest thing I have found to a documentation of a strategy. All sequencing papers I have found will describe the pipeline and filters to some degree, but then do not touch the topic of manual review and why they would exclude some of the variants.

Can someone in this community point me towards a publication or share their 'secret sauce' in terms of manual review strategies?

Thanks, O.
onconaut is offline   Reply With Quote
Old 01-22-2015, 08:51 AM   #2
Senior Member
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503

'Looks good' is in the eye of the beholder, but common metrics include sequencing depth (more is better), variant present on reads from both strands (strand-specific variants are more likely to be false-positives), mapping quality, and complexity of the alignment (i.e., nearby indels increase the likelihood of false-positive SNP calls).

Blue Collar Bioinformatics blog (here) has benchmarked several variant-calling workflows (including GATK best practices) against the NIST standard Genome-in-a-Bottle. Data and workflows can be downloaded/replicated, so you can see for yourself what constitutes 'good' and 'bad'-looking variant calls.
HESmith is offline   Reply With Quote

dry tech, igv, quality control, vcf

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 05:22 AM.

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