I16 Tag In Vcf File - Samtools Mpileup

Question

[aswathyseb]

Hi, I do not have I16 tag in my VCF file while calling snp using samtools mpileup |bcftools. Does anyone know how to have this tag in INFO field? what options should I use while running the snp call to get this tag in the output?

Thank you very much

-AS

[sa9]

using "bcftools view" without option outputs I16 values as in:

samtools mpileup -gDSf g1k_v37.fasta file.bam | bcftools view -

but you don't get the I16 if you add arguments to the "bcftools view" (e.g -gcv) , AFAIK.

[aswathyseb]

Thank you very much...:) It was very helpful..