Error in Bam with Freec Control

agraz

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Join Date: Nov 2014

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Error in Bam with Freec Control

04-01-2016, 05:40 AM

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 http://bioinfo-out.curie.fr/projects...al.html#CONFIG

Using matesOrientation=0

Code:

[general] chrLenFile = /folder/chr19.len coefficienteOfVariation = 0.062 ploidy = 2,3,4 window = 50000 chrFiles= /folder/hg19_per_coordenates outputDir = ./ degree = 3&4 intercept = 1 sex=XY breakPointType=4 [sample] mateFile = /folder/x.bam inputFormat = bam matesOrientation = 0 [BAF] SNPfile = /folder/hg19_snp142.SingleDiNucl.1based.txt minimalCoveragePerPosition = 5

Last edited by agraz; 04-01-2016, 05:41 AM. Reason: confidential information
Tags: cnv, control-freec, freec

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