The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

how to understand the annotation and numbers in GATK-generated VCF?

rcholicrcholic DenverMember Posts: 68

I have been trying to find documentation for understanding the annotations and numbers in the VCF file. Something like below, can someone guide me how to understand/interpret the numbers? How is the quality of the variant calling for this particular indel?

AC=2;
AF=0.100;
AN=20;
BaseQRankSum=6.161;
ClippingRankSum=-2.034;
DP=313;
FS=5.381;
InbreedingCoeff=-0.1180;
MLEAC=2;
MLEAF=0.100;
MQ=58.49;
MQ0=0;
MQRankSum=-0.456;
QD=1.46;
ReadPosRankSum=-4.442;
VQSLOD=0.348;
topculprit=ReadPosRankSum

Answers

Sign In or Register to comment.