Question: Annotation format for SNVs
0
gravatar for Hamid
13 months ago by
Hamid10
Hamid10 wrote:

Hello Biostars, I have a SNV annotations for a number of genes. They look like this: https://ufile.io/hyvs4

Can someone shed some light on this and tell me, 1. Why there are 3 rows for each position? 2. What software generates this type of annotation? 3. What is each column? I assume it is a standard format.

Thanks

snp snv • 286 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by Hamid10

Here is some output for the others to see:

16,56359179,G,G,A,SNV,0,FALSE,TRUE,Transcript,INTRONIC,2,intron,0.56,0.08,0,0,NA,0.031,0.019,0.026,-1.262,-1.243,-1.185,0.199,-0.397,NA,NA,797,-73,-2.12,0.10,1.46,-0.90,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98888,9509,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,-0.389122,0.411
16,56359179,G,G,C,SNV,0,TRUE,TRUE,Transcript,INTRONIC,2,intron,0.56,0.08,0,0,NA,0.031,0.019,0.026,-1.262,-1.243,-1.185,0.199,-0.397,NA,NA,797,-73,-0.57,0.33,-0.90,5.17,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98888,9509,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,-0.712846,0.067
16,56359179,G,G,T,SNV,0,TRUE,TRUE,Transcript,INTRONIC,2,intron,0.56,0.08,0,0,NA,0.031,0.019,0.026,-1.262,-1.243,-1.185,0.199,-0.397,NA,NA,797,-73,0.95,0.55,-1.43,8.40,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98888,9509,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,-0.652688,0.093
16,56359180,G,G,A,SNV,0,FALSE,TRUE,Transcript,INTRONIC,2,intron,0.57,0.08,0,0,NA,0.037,0.025,0.033,0.300,0.294,0.303,0.199,0.199,NA,NA,797,-77,-1.44,0.05,1.03,-1.58,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98889,9508,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,0.062257,3.209
16,56359180,G,G,C,SNV,0,TRUE,TRUE,Transcript,INTRONIC,2,intron,0.57,0.08,0,0,NA,0.037,0.025,0.033,0.300,0.294,0.303,0.199,0.199,NA,NA,797,-77,-0.27,0.43,-0.62,4.04,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98889,9508,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,-0.280606,0.735
16,56359180,G,G,T,SNV,0,TRUE,TRUE,Transcript,INTRONIC,2,intron,0.57,0.08,0,0,NA,0.037,0.025,0.033,0.300,0.294,0.303,0.199,0.199,NA,NA,797,-77,1.58,0.49,-0.32,3.69,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98889,9508,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,-0.112431,1.639
16,56359181,G,G,A,SNV,0,FALSE,TRUE,Transcript,INTRONIC,2,intron,0.57,0.08,0,0,NA,0.041,0.030,0.039,0.300,0.294,0.303,0.199,0.199,NA,NA,797,-72,-2.01,0.08,2.06,-1.01,NA,NA,NA,NA,0.053666,0.000,0.000,0.000,0.008,0.197,0.000,0.079,0.000,0.000,0.000,0.000,0.000,0.008,0.134,0.575,NA,3.24,3.00,1.00,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,R0,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,98890,9507,ENSG00000087258,ENST00000262494,CCDS10757.1,GNAO1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,3/7,NA,NA,NA,NA,NA,NA,NA,0.027573,2.856

Well, let's do some investigating here. From where did you obtain the file? Learning that may indirectly inform you of how it was produced.

ADD REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe52k
0
gravatar for Hamid
13 months ago by
Hamid10
Hamid10 wrote:

Thanks, I found the header actually, for now, my main question is why do we have 3 lines per each snp? And what is the Ref and what is the Anc. The header for the first few columns is: Chrom Pos Ref Anc Alt Type Length

ADD COMMENTlink written 13 months ago by Hamid10
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