Try to identify pindel output fields containing info related to Read Depth (mutated allele) and Reference Depth?

[ipstone]

Hello,

I am wondering what field/s in the pindel vcf output, are related to 'Allele Depth' (to calculate 'Allele Depth') and 'Reference Depth' ?

Using cgpPindel (through docker), my output vcf has the following fields:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PP,Number=1,Type=Integer,Description="Pindel calls on the positive strand">
##FORMAT=<ID=NP,Number=1,Type=Integer,Description="Pindel calls on the negative strand">
##FORMAT=<ID=PB,Number=1,Type=Integer,Description="BWA calls on the positive strand">
##FORMAT=<ID=NB,Number=1,Type=Integer,Description="BWA calls on the negative strand">
##FORMAT=<ID=PD,Number=1,Type=Integer,Description="BWA mapped reads on the positive strand">
##FORMAT=<ID=ND,Number=1,Type=Integer,Description="BWA mapped reads on the negative strand">
##FORMAT=<ID=PR,Number=1,Type=Integer,Description="Total mapped reads on the positive strand">
##FORMAT=<ID=NR,Number=1,Type=Integer,Description="Total mapped reads on the negative strand">
##FORMAT=<ID=PU,Number=1,Type=Integer,Description="Unique calls on the positive strand">
##FORMAT=<ID=NU,Number=1,Type=Integer,Description="Unique calls on the negative strand">
##FORMAT=<ID=FD,Number=1,Type=Integer,Description="Fragment depth">
##FORMAT=<ID=FC,Number=1,Type=Integer,Description="Fragment calls">

I am trying to calculate the AD field for the subsequent filters using AD field. I am wondering whether RP+NP would be the Allele Depth?

The followings are what I see in a much older pindel output fields:

##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">

Thanks!

Isaac