VEP result table, REF, ALT, CSQ meaning.

Question

[dirranrak]

Hi all,

I got this result from VEP, I have some SNPs in the forward strand (1), reverse strand (-1) and no strand indication. I have these questions that I did not find the answers:

1. Which of the REF or ALT allele is the minor or major allele?
2. What is the CSQ?
3. Why I have SNPs that have not been assigned to a strand and how can I fix it?

Thank you.

Chr  Position   ID                    REF   ALT  info   Strand 
1   864627  rs6681049   T   A,C CSQ=A   -1
9   138172039   rs9314655   G   A   CSQ=A   1
1   989518  rs6665000   C   A   CSQ=A

[GenoMax]

It would be useful to include your VEP command line options (if you ran it that way).

[dirranrak]

Hi Genomax2,

I just submitted the data at the website and their VEP command is

perl variant_effect_predictor.pl --appris --biotype --check_existing --gmaf --maf_1kg --maf_esp --maf_exac --polyphen both --pubmed --regulatory --sift both --species homo_sapiens --symbol --tsl --cache --input_file [input_data]

[GenoMax]

Emily_Ensembl

I am going to tag @Emily from Ensembl who may be the best person to answer this question.

[dirranrak]

Thank you Genomax2, I hope to finish my standardization data as soon as possible and switch to next step of my analysis.