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Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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ERROR: need a bed file with exon coordinates #70

Open yueyangtime opened 5 years ago

yueyangtime commented 5 years ago

Hi, I am working on using FREEC to call CNVs, I have used the following config file:

[general]
BedgraphOutput=FALSE
breakPointThreshold=1.2
breakPointType=2
bedtools=/FAH/data1/bioinfo/SOFTWARE/install/bedtools2/bin/bedtools
chrFiles=/FAH/data1/bioinfo/DATABASE/hg19/ref/chr_fa
chrLenFile=/FAH/data1/bioinfo/PMO/xieyueyang/config/Control_Freec_config/h19.fa.fai
samtools=/FAH/data1/bioinfo/SOFTWARE/install/samtools-1.7/samtools
contamination = 0.00
contaminationAdjustment = TRUE
coefficientOfVariation =0.062
forceGCcontentNormalization = 1
intercept = 0
minimalSubclonePresence = 30
minCNAlength = 5
maxThreads = 16
degree = 1
ploidy = 2,3,4
noisyData=TRUE
printNA=FALSE
readCountThreshold = 50
sex = XX
window = 0
outputDir=/FAH/data1/bioinfo/PMO/xieyueyang/Analy_double1029/CNV_FREEC/
maxThreads=16

[sample]

mateFile = /FAH/data1/bioinfo/PMO/xieyueyang/Analy_double1029/recall_gatk4/EQA201911.recal.bam
inputFormat = BAM
mateOrientation = FR

[control]
mateFile = /FAH/data1/bioinfo/PMO/xieyueyang/Analy_double1029/recall_gatk4/EQA2019NC.recal.bam
inputFormat = BAM
mateOrientation = FR

[BAF]

SNPfile=/FAH/data1/bioinfo/DATABASE/FreeC/hg19_snp142.SingleDiNucl.1based.txt
makePileup=/FAH/data1/bioinfo/PMO/xieyueyang/data/hg19_snp142.SingleDiNucl.1based.bed
fastaFile=/FAH/data1/bioinfo/DATABASE/hg19/ref/ucsc.hg19.fasta
minima1CoveragePerPosition=8
minimalQualityPerPosition=8
shiftInQuality=33

[tatget]

captureRegions=/FAH/data1/bioinfo/PMO/xieyueyang/Analy_double1111/CNV_ANACONDA_output/EQA201911/Results/FREEC/targets.bed

but, I get the following error/segfault:

ERROR : You set window=0. Did you mean that your data come from whole exome sequencing?
In this case, you should provide a bed file with exon coordinates (see manual on the Control-FREEC website)
If you data are whole genome sequencing data either provide a positive window size or use a coefficient of variantion to infer window size

but I did provide the bed file in [tatget] captureRegions, is there anything wrong? Thanks, yueyang

yueyangtime commented 5 years ago

here is my bed file:

$ head /FAH/data1/bioinfo/PMO/xieyueyang/Analy_double1111/CNV_ANACONDA_output/EQA201911/Results/FREEC/targets.bed
chr1    2488098 2488177 
chr1    2489159 2489278 
chr1    2489776 2489912 
chr1    2491256 2491422 
chr1    2492057 2492158 
chr1    2493106 2493259 
chr1    2494298 2494340 
chr1    2494581 2494717 
chr1    6246726 6246881 
chr1    6252984 6253119
abedkurdi commented 4 years ago

maybe you have to fix the typo only: target instead of tatget

valeu commented 4 years ago

Right. it should be target. Did it work?