vcf file

Question

[karthivalarmathi99]

this is my vcf file i don't understand MAXGT and POLY. i am go to gwas study but this MAXGT AND POLY column plink take sample column . maxgt and poly any one column remove I'm going to gwas analysis . any one explaion how to go this vcf file gwas analysis. Kevin Blighe

##fileformat=VCFv4.1                                        
##fileDate=20130319                                     
##source=GenerateReportDataAndVCFv2.2.2.0                                       
##reference=HumanNCBI37_UCSC                                        
##phasing=none                                      
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">                                      
##INFO=<ID=TI,Number=.,Type=String,Description="Transcript ID">                                     
##INFO=<ID=GI,Number=.,Type=String,Description="Gene ID">                                       
##INFO=<ID=EXON,Number=0,Type=Flag,Description="Exon Region">                                       
##INFO=<ID=FC,Number=.,Type=String,Description="Functional Consequence">                                        
##FILTER=<ID=q20,Description="Quality below 20">                                        
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">                                        
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">                                       
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  12AD50320_MAXGT 12AD50320_POLY
chr16   60054   rs62028702  A   C   23  PASS    DP=9    GT:GQ   0/1:23  0/1:56
chr16   60087   rs62028703  C   G   27  PASS    DP=13   GT:GQ   0/1:27  0/1:60
chr16   60095   rs62028704  G   T   26  PASS    DP=13   GT:GQ   0/1:26  0/1:59
chr16   60120   .   G   A   11  q20 DP=10   GT:GQ   1/0:11  1/0:43

[GenoMax]

Looks like you had asked this question in a previous thread: vcf problem removing MAXGT and POLY

Please do not post the same questions in multiple threads.

[Pierre Lindenbaum]

12AD50320_MAXGT 12AD50320_POLY are the samples. Why do you have those names is dependent of your upstream analysis.

[karthivalarmathi99]

i have download data for adni website . i don't know explain sir. maxt and ploy which one i take it go for gwas study. Pierre Lindenbaum

[Pierre Lindenbaum]

I don't know what is adni website. Nevertheless I don't know what is the nature of a random VCF found on the web, you should ask the provider.

Answer 1

[DBScan]

12AD50320_MAXGT and 12AD50320_POLY are your sample names.