VCF lacking mandatory header after variant calling with samtools

Question

[punittyagi88]

i had done snp calling using bwa ,samtools on Ustilago Maydis. i got vcf file which donot have the mandatory header lines but have the header starting with CHROM,Pos,Ref,etc.please help me out i have done with google but dont know why this happen. this is haeder.

Chrom   Position    Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-:pval   SamplesRef  SamplesHet  SamplesHom  SamplesNC   Cons:Cov:Reads1:Reads2:Freq:P-value

thanks in advance.

[ATpoint]

Without the original command line, no one can really help you.

[WouterDeCoster]

Hello punittyagi88,

This thread would benefit from a more accurate title. Just using "variants calling file" doesn't say anything about the content of your question, instead using for example "VCF lacking mandatory header after variant calling with samtools" is far more informative and will quicker attract people who can help you with your issue. I have updated your post with the new title. Please keep this in mind when creating new posts.

Cheers, Wouter

[punittyagi88]

Thanks Wouter. Iam new to NGS Family.So Learn from Experienced people like you.

[Pierre Lindenbaum]

if the header is

Chrom   Position    Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-:pval   SamplesRef  SamplesHet  SamplesHom  SamplesNC   Cons:Cov:Reads1:Reads2:Freq:P-value

then it is NOT a vcf file...

[pragathi.sneha91]

I am facing the same problem. how did u resolve it