BAF and estimatedBAF

[gianfilippo]

Hi,

I am trying to add some info (see below) to a variant file (from Mutect2 analysis) for downstream analysis
copy number of non-tumor cells in the sample at each mutation locus
copy number of the minor allele in the malignant cells
copy number of the major allele in the malignant cell or total copy number of tumor cells

I ran control-FREEC with paired Tumor-Normal and have
.tumor.mpileup.gz_normal_ratio.txt
.tumor.mpileup.gz_normal_CNVs
.tumor.mpileup.gz_ratio.txt
.tumor.mpileup.gz_CNVs

I believe I need the BAF and the CopyNumber to derive everything I need, intersecting the variants with the control-FREEC windows in the .tumor.mpileup.gz_ratio.txt file.

Could you please explain how the BAF and estimatedBAF are derived ?
I understand the inferred Genotype reflects the estimatedBAF, so I assume using estimatedBAF should be ok ?

Could you please clarify the _normal files as far as Ratio is concerned ?

Thanks