FREEC Your GC-content file is empty or is in a wrong format

Question

[marcoabbestia]

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!

Please I need some help to understand what I wrong. Any suggestion will be very appreciated. Greetings Marco

[marcoabbestia]

Thanks Kevin for your reply. I tried with a chromosome to test if it is work and now it is fine greetings Marco

Answer 1

[Kevin Blighe]

Instead of supplying a GCcontentProfile file, you can just supply a directory of FASTA files, with 1 file per contig. Obviously the names must match the contig names in your input BAMs. For example:

chrFiles=/refs/hg19/chromosomes/

File listing:

ls -1 /refs/hg19/chromosomes/
chr10.fa
chr11.fa
chr11_gl000202_random.fa
chr12.fa
chr13.fa
chr14.fa
chr15.fa
chr16.fa
chr17_ctg5_hap1.fa
chr17.fa
chr17_gl000203_random.fa
chr17_gl000204_random.fa
chr17_gl000205_random.fa
chr17_gl000206_random.fa
chr18.fa
chr18_gl000207_random.fa
chr19.fa
chr19_gl000208_random.fa
chr19_gl000209_random.fa
chr1.fa
chr1_gl000191_random.fa
chr1_gl000192_random.fa
chr20.fa
chr21.fa
chr21_gl000210_random.fa
chr22.fa
chr2.fa
chr3.fa
chr4_ctg9_hap1.fa
chr4.fa
chr4_gl000193_random.fa
chr4_gl000194_random.fa
chr5.fa
chr6_apd_hap1.fa
chr6_cox_hap2.fa
chr6_dbb_hap3.fa
chr6.fa
chr6_mann_hap4.fa
chr6_mcf_hap5.fa
chr6_qbl_hap6.fa
chr6_ssto_hap7.fa
chr7.fa
chr7_gl000195_random.fa
chr8.fa
chr8_gl000196_random.fa
chr8_gl000197_random.fa
chr9.fa
chr9_gl000198_random.fa
chr9_gl000199_random.fa
chr9_gl000200_random.fa
chr9_gl000201_random.fa
chrM.fa
chrUn_gl000211.fa
chrUn_gl000212.fa
chrUn_gl000213.fa
chrUn_gl000214.fa
chrUn_gl000215.fa
chrUn_gl000216.fa
chrUn_gl000217.fa
chrUn_gl000218.fa
chrUn_gl000219.fa
chrUn_gl000220.fa
chrUn_gl000221.fa
chrUn_gl000222.fa
chrUn_gl000223.fa
chrUn_gl000224.fa
chrUn_gl000225.fa
chrUn_gl000226.fa
chrUn_gl000227.fa
chrUn_gl000228.fa
chrUn_gl000229.fa
chrUn_gl000230.fa
chrUn_gl000231.fa
chrUn_gl000232.fa
chrUn_gl000233.fa
chrUn_gl000234.fa
chrUn_gl000235.fa
chrUn_gl000236.fa
chrUn_gl000237.fa
chrUn_gl000238.fa
chrUn_gl000239.fa
chrUn_gl000240.fa
chrUn_gl000241.fa
chrUn_gl000242.fa
chrUn_gl000243.fa
chrUn_gl000244.fa
chrUn_gl000245.fa
chrUn_gl000246.fa
chrUn_gl000247.fa
chrUn_gl000248.fa
chrUn_gl000249.fa
chrX.fa
chrY.fa

-----------------------------------------------

If you insist on going the route of creating your own GCcontentProfile file, then it has to adhere to the following format (tab-delimited):

• chromosome
• start position
• GC-content
• percentage of ACGT-letter per window (1-poly(N)%)

The values are tied up with your specified window size, too.

I think that it's just easier to supply the FASTA files via chrFiles and go that route.

Kevin