Which type of Annotation is QD, FS, MQ, MQRankSum, ReadPosRankSum, SOR.

Question

[yoh1242]

Hello, According to Annovar their is gene, region and filter based annotation. To which category does QD, MQ, SOR etc annotation performed by GATK VariantAnnotation falls under. Other then GATK VariantAnnotation is their any other tool which can perform this type of annotation.

Answer 1

[Kevin Blighe]

I believe you are confusing 2 different things:

• annotation of genetic variants with ANNOVAR
• key-value pairings as tags in a VCF

The definitions of QD, MQ, and SOR will be in your VCF header.

Kevin