How to add both DP and DV format tags to a VCF file

[Sfunkhouser]

Using samtools mpileup -D, (and bcftools view) I have been able to generate VCF files with the samples having the "DP" format tag. This appears to be giving me the total reads per sample for a given site but does not differentiate between reads mapped to reference or variant.

For this I would like my output to include the "DV" tag which is supposed to indicate: "# high-quality non-reference bases".

How can I specify that I need the DV tag? Samtools mpileup -D is only giving me DP, not DV.

Scott

[lre1234]

If you are using samtools v1.0 there is this option:

-t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP

[Sfunkhouser]

Thanks. Seems like everyone is on board with v1.0 now so I'll make the switch too.