[Samtools-help] Samtools variant without annotation in VCF

[mehar <meh...@he...>]

Hi all,


I have used samtools for variant calling with the below command:

samtools mpileup -ABugf  ref.fa -l target.bed -d 1000000 input.bam | 
bcftools view -vcg - | vcfutils.pl varFilter -D 1000000 > SAM.vcf

Some variants do not have the information after column 6. Below is an 
example:

$ grep "62105986" SAM.vcf
chr2    62105986    .    C    T    221

I could not do further analysis with other tools because of this missing 
information. Could someone comment why this happens? and ways to fix 
this. Thanks

Br
Mehar