I'm trying to estimate LOH using purity, ploidy estimates from sequenza.

I use cnvkit call option with its default thresholds,

conda activate **cnvkit0.9.7**
cnvkit.py call $tumour_id.recalibrated.cns -y -v $mutect_tumour_dir/$tumour_id/$tumour_id.passed.vcf.gz --purity $purity --ploidy $ploidy -o $tumour_id.call.cns

The output gives me -ve BAF values which im not sure how to interpret

  chromosome    start      end        gene                                                      log2       baf  cn  cn1 cn2   depth probes  weight
chr16 66669013 69943499 CMTM4,DYNC1LI2,DYNC1LI2,LOC106699570,LOC106699570,LOC106699570,TERB1  -0.871623 -0.211176  1   1   0 71.7805   2818 2418.18

To confirm are LOH regions where cn1!=cn2 and BAF=0. Also what about estimating copy number netural LOH.

Thank you.