Question: VEP result table, REF, ALT, CSQ meaning.
0
gravatar for dirranrak
3.8 years ago by
dirranrak10
United States
dirranrak10 wrote:

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
snp vep assembly • 1.6k views
ADD COMMENTlink modified 6 months ago by zx87548.8k • written 3.8 years ago by dirranrak10

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

ADD REPLYlink written 3.8 years ago by genomax76k

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]
ADD REPLYlink modified 6 months ago by zx87548.8k • written 3.8 years ago by dirranrak10

Emily_Ensembl

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

ADD REPLYlink written 3.8 years ago by genomax76k

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

ADD REPLYlink written 3.8 years ago by dirranrak10
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