Error: to calculate BAF values

[ghost]

Error: to calculate BAF values, you need to provide mateFile in SAMtools pileup format
Or you can set 'makePileup' parameter true by providing a path to a VCF file with SNP position

`###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###

[general]
chrLenFile = /${path}/freec/ucsc.hg19.fasta.fai
window = 0
ploidy = 2
outputDir = ${path}/freecv1/

BedGraphOutput=TRUE
bedtools=${path}/bedtools/bedtools-2.30.0/bin/bedtools

#sex=XY
breakPointType=4
chrFiles = ${path}/database/hg19/gatk_bundle/ref_split/

maxThreads=20

breakPointThreshold=0.1
noisyData=FALSE
printNA=FALSE

readCountThreshold=50

[sample]

mateFile = ${path}/s3-2_normal.final.bam
inputFormat = BAM
mateOrientation = FR

[control]

mateFile = ${path}/s3-2_tumor.final.bam
inputFormat = BAM
mateOrientation = FR

[BAF]

SNPfile = ${path}/hg19/gatk_bundle/dbsnp_138.hg19.vcf
minimalCoveragePerPosition = 5

[target]

captureRegions = ${path}/freecv1/ucsc.hg19.bed
makePileup = ${path}/freec/hg19_snp142.SingleDiNucl.1based.bed
SNPfile = ${path}/freec/hg19_snp142.SingleDiNucl.1based.txt
bedtools = ${path}/bedtools/bedtools-2.30.0/bin/bedtools
samtools = ${path}/samtools/samtools-1.13/samtools`

[valeu]

set
makePileup=${path}/hg19/gatk_bundle/dbsnp_138.hg19.vcf

and it should work

[ghost]

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