about adding MISSING fields TO VCF files

Question

[Bogdan]

Dear all,

when working with VCF files, if a VCF file (coming from a specific aligner) misses some important fields that are used for filtering i.e. DP4, MQ, SB (strand bias) etc, how could I add these missing fields to the VCF file (based on aligned BAM files (normal, and tumor), and reference sequence). Thanks,

-- bogdan