BAF > 0 when CopyNumber = 0

[gianfilippo]

Hi,

I am running my analysis using paired Tumor-Normal samples.

Looking at the .tumor.mpileup.gz_ratio.txt I find calls with BAF > 0 when CopyNumber = 0

Are these expected artifacts ?

Thanks

[gianfilippo]

i should add that I intersect the control-FREEC .tumor.mpileup.gz_ratio.txt file with the mutect2 output VCF to add copynumber info to variant calls. The issue I see is in windows overlapping variant calls, so that there are reads. Below is an example of the merged file and control-FREEC .tumor.mpileup.gz_ratio.txt file
CHROM POS trinucleotide var_counts ref_counts total_counts c_tumor_minor c_tumor_major c_normal
chr14 105845439 26 4 2 6 0 1 2
chr14 106116756 63 2 7 9 0 0 2
chr14 106116758 32 2 7 9 0 0 2
chr14 106207188 69 7 15 22 0 0 2

Chromosome Start Ratio MedianRatio CopyNumber BAF estimatedBAF Genotype UncertaintyOfGT Subclone_CN Subclone_Population
14 106114412 -1 0.101338 0 -1 2 0 -1 1 0.319902
14 106116255 0.0987396 0.101338 0 -1 2 0 -1 1 0.319902
14 106118098 -1 0.101338 0 -1 2 0 -1 1 0.319902