Question: I16 Tag In Vcf File - Samtools Mpileup
gravatar for aswathyseb
6.5 years ago by
aswathyseb30 wrote:

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


samtools mpileup • 3.0k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 6.5 years ago by aswathyseb30

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.

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by sa9810

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

ADD REPLYlink written 6.5 years ago by aswathyseb30
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