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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Your GC-content file is empty or is in a wrong format Please use chomosome sequences (option "chrFiles") to recreate it! #46

Open marcotolone opened 5 years ago

marcotolone commented 5 years ago

Hi, I'd like to use FREEC without control to detect CNV in goat genome. I prepared my chromosome lenght file (goat_chr.len), my GC_content file, without mappability using bedtools on goat genome (example_GC_content.txt) and I prepared my config file: [general] chrLenFile = /illumina/runs/DNAPipeline/girgentana1/goat_chr.len ploidy = 2 GCcontentProfile = /illumina/runs/DNAPipeline/girgentana1/GC_girgentana_mod.cnp window = 50000 minExpectedGC = 0.30 maxExpectedGC = 0.70

[sample]

mateFile = /illumina/runs/DNAPipeline/outRD.bam inputFormat = BAM mateOrientation = 0

[control]

I run FREEC and after reading the bam file It gives me the error: Your GC-content file /illumina/runs/DNAPipeline/girgentana1/GC_girgentana_mod.cnp is empty or is in a wrong format

Please use chomosome sequences (option "chrFiles") to recreate it!

I have attached the chromosome lengths file, an example of GC content file and the log.txt with some information of the analysis. Please I need some help to understand what I wrong. Any suggestion will be very appreciated. Greetings Marco

example_GC_content.txt goat_chr.txt log.txt

valeu commented 5 years ago

Dear Marco, you should delete or comment your CG-content file (which is optional), and provide instead a path to fasta files with chromosomes (chr1.fa, chr2.fa etc)

#GCcontentProfile = /illumina/runs/DNAPipeline/girgentana1/GC_girgentana_mod.cnp
chrFiles=/pathToGoatGenome/Chromosomes/
marcotolone commented 5 years ago

Dear Valentina thank you very much for your answer. I tried with one chromosome in fasta within a folder (chrFiles) and now it is work! thanks again greetings Marco