VCF lacking mandatory header after variant calling with samtools
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.
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punittyagi88 •
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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
Thanks Wouter. Iam new to NGS Family.So Learn from Experienced people like you.
if the header is
then it is NOT a vcf file...
I am facing the same problem. how did u resolve it
Without the original command line, no one can really help you.