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Old 04-01-2016, 05:40 AM   #1
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Location: santander

Join Date: Nov 2014
Posts: 2
Default Error in Bam with Freec Control

Hi all!
I'm looking for information with errors in free control. My problem is the next:
Freec/prueba/x.bam read in 216 seconds [fillMyHash]
108642670 lines read..
0 reads used to compute copy number profile

Error: FREEC was not able to extract reads from /folder/x.bam

Check your parameters: inputFormat and matesOrientation
Use "matesOrientation=0" if you have single end reads
Check the list of possible input formats at

Using matesOrientation=0

chrLenFile = /folder/chr19.len
coefficienteOfVariation = 0.062
ploidy = 2,3,4
window = 50000
chrFiles= /folder/hg19_per_coordenates

outputDir = ./

degree = 3&4
intercept = 1



mateFile = /folder/x.bam

inputFormat = bam
matesOrientation = 0


SNPfile = /folder/hg19_snp142.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5

Last edited by agraz; 04-01-2016 at 05:41 AM. Reason: confidential information
agraz is offline   Reply With Quote

cnv, control-freec, freec

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