Error: to calculate BAF values
Opened this issue · 2 comments
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 = ${path}/samtools/samtools-1.13/samtools`
set
makePileup=${path}/hg19/gatk_bundle/dbsnp_138.hg19.vcf
and it should work