Set contaminationAdjustment = TRUE but freec still reports "FREEC is not going to adjust profiles for a possible contamination by normal cells"

[riyuebao]

Hello - I have whole exome data of tumor/normal BAMs ready and in config file, I set contaminationAdjustment = TRUE but in log file freec still reports "FREEC is not going to adjust profiles for a possible contamination by normal cells". As a result, the output tumor purity is 1.

Is there other options that I need to set in order to ask freec to run this contamination adjustment?

I don't have a pre-estimated contamination value available, and hopes freec could evaluate it by itself by setting contaminationAdjustment = TRUE.

Here is my config file

"###For more options see: tutorial.html#CONFIG ###

[general]

BedGraphOutput = TRUE bedtools = bedtools breakPointThreshold = 1.2 ## default is 0.8 breakPointType = 4 chrFiles = chrLenFile = GRCh38.d1.vd1.S07604624_V6UTRr2_Covered.picard.hg38.merged.srt.exRandom_Alt.ex_Un.col1_2.chromsize coefficientOfVariation = 0.05 contaminationAdjustment = TRUE ## it will automatically evaluate and correct for the contamination degree = 1 ## control-read-count-based normalization, WES forceGCcontentNormalization = 1 ## normalize the sample and the control RC using GC-content and then calculate the ratio "Sample contol RC" intercept = 1 ## 1 or 0??? minCNAlength = 5 ## default is 3 minMappabilityPerWindow = 0.85 minimalSubclonePresence = 30 ## detects subclones present in x% of cell population maxThreads = 8 noisyData = TRUE outputDir = ploidy = 2,3,4 printNA = FALSE readCountThreshold = 50 ## recommended value >=50 for for exome data sambamba = sambamba samtools = samtools sex = XY window = 0 ## for WES telocentromeric = 50000

[sample]

mateFile = tumor.bwamem.merged.dedup.recal.rmdup.bam inputFormat = BAM mateOrientation = FR

[control]

mateFile = normal.bwamem.merged.dedup.recal.rmdup.bam inputFormat = BAM mateOrientation = FR

[BAF]

makePileup = dbsnp_146.hg38.bed fastaFile = GRCh38.d1.vd1.fa minimalCoveragePerPosition = 10 minimalQualityPerPosition = 20 shiftInQuality = 33 SNPfile = dbsnp_146.hg38.vcf.gz minimalCoveragePerPosition = 5

[target]

captureRegions = S07604624_V6UTRr2_Covered.picard.hg38.merged.srt.exRandom_Alt_Un.bed "

Thanks in advance.

best, Riyue

[riyuebao]

BTW using version 11.5

[riyuebao]

I figured it out. It was because I had this comment line after the value. After removing the comment line freec works as expected. contaminationAdjustment = TRUE

[riyuebao]

Thanks to @kmhernan for the help!