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Annotation format for SNVs
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Entering edit mode
2.7 years ago
Hamid ▴ 10

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

snv SNP • 484 views
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Entering edit mode

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.

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Entering edit mode
2.7 years ago
Hamid ▴ 10

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