vcf problem removing MAXGT and POLY

Question

[karthick]

this is my vcf file i don't understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my problem . pls any one help me.

##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

[Pierre Lindenbaum]

12AD50320_MAXGT 12AD50320_POLY are the name of the samples, this is was set by your upstream command(s).

[4galaxy77]

Please choose a more descriptive title and tag

[Pierre Lindenbaum]

of course you have a problem. Please, change the title.

Answer 1

[Pierre Lindenbaum]

while it works, it's safer to use bcftools view -G in.vcf -o output_file.vcf

[karthick]

thanks for your response sir @Pierre Lindenbaum

[ATpoint]

Would you now please do what others have asked to fulfill the minimum standards for this question? Use a reasonable title, please upvote and accept answers if helpful. That is the least you can do given you expect others to help you.

[Pierre Lindenbaum]

Please accept the answer so the question is marked solved on the website. To do that, click on the green check mark on the left side of the answer.

[karthick]

bcftools view -G in.vcf -o output_file.vcf

this command I'm used MAXGT AND POLY column removed but how to going GWAS study without sample column information like genotype(GT) and genotype Quality(GQ)information.

This is output result sir

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
chr16   60054   rs62028702  A   C   23  PASS    DP=9
chr16   60087   rs62028703  C   G   27  PASS    DP=13
chr16   60095   rs62028704  G   T   26  PASS    DP=13
chr16   60120   .   G   A   11  q20 DP=10

Please solve this sir

Answer 2

[Umer]

Your question is not so descriptive but based on the hint of GWAS i think you might want to remove both columns completly.

SO, if you want to remove whole columns 12AD50320_MAXGT and 12AD50320_POLY assuming you are using linux terminal then use

cut -f 1-9 input_file.vcf > output_file.vcf

[Ram]

No. From the question, it's obvious the user is not bioinformatics savvy. Don't give them unsafe commands. Use well tested tools like bcftools as Pierre recommends.