ANNOVAR annotation

[bloodyhole]

I am using ANNOVAR to annotate variants called last night. I am pretty much new to Bioinformatics, Biology..so please bear in mind

Could anyone explain specific things in my annovar output?

1. If there is a just blank in a 1000G filter column, what does it mean?
Do I need to consider these genes for prioritization?

2. What do they mean, such as
./., 0/0, 0/1, 1/1, 1/2, 2/2?

3. If there is a blank or 'unknown' in Exonic function, do I need to consider these for possible genes that I will be interested? or just care about non-synonymous ?


Sorry, it is really really basic, but I am just trying to learn these by myself. Can anyone help me?

[bb420]

Hello

I may require some more info from you to answer the question..

1. If there is a just blank in a 1000G filter column, what does it mean?
Do I need to consider these genes for prioritization?

A: what is the command used? do you mean summarize_annovar? If so, it just means not observed in 1000G.

2. What do they mean, such as
./., 0/0, 0/1, 1/1, 1/2, 2/2?

A: what is the command used? what is this from exactly? This may be specific to your 1000G data set.

3. If there is a blank or 'unknown' in Exonic function, do I need to consider these for possible genes that I will be interested? or just care about non-synonymous ?


A: this is due to lack of complete ORF information for the gene, so even though the variant is located within an exon, it is unknown which amino acid is changed.

Bhanu