Control-FREEC error bed file

Question

[2nelly]

Hi all, I am trying to use Control-FREEC to detect CNV. It seems that I am facing an issue with my bed file(mouse genome) since i am getting an annoying error that my target file is not bed and not sorted but it is. Please see the error and the first few lines of my bed file below. The m letter in front chr stands for mouse, and all my files, reference bam e.t.c. use this motif. Any suggestions fellas?

..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m1 : 0
..Reading /home/vdionellis/Desktop/files_for_cnv/mm10_targets.bed
..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m2 : 0
..Reading /home/vdionellis/Desktop/files_for_cnv/mm10_targets.bed
..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m3 : 0
..Reading /home/vdionellis/Desktop/files_for_cnv/mm10_targets.bed
..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m4 : 0
..Reading /home/vdionellis/Desktop/files_for_cnv/mm10_targets.bed
..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m5 : 0
..Reading /home/vdionellis/Desktop/files_for_cnv/mm10_targets.bed
..Your file must be in .BED format, and it must be sorted
Number of exons analysed in chromosome m6 : 0


mchr1   3205903 3206185 -
mchr1   3206185 3206468 -
mchr1   3206468 3206751 -
mchr1   3206751 3207034 -
mchr1   3207034 3207316 -
mchr1   3213438 3213712 Xkr4
mchr1   3213712 3213986 Xkr4
mchr1   3213986 3214260 Xkr4
mchr1   3214260 3214535 Xkr4
mchr1   3214535 3214809 Xkr4
mchr1   3214809 3215083 Xkr4
mchr1   3215083 3215357 Xkr4
mchr1   3215357 3215632 Xkr4
mchr1   3215632 3215899 Xkr4
mchr1   3215899 3216166 Xkr4
mchr1   3216166 3216433 Xkr4
mchr1   3216433 3216700 Xkr4
mchr1   3216700 3216968 Xkr4
mchr1   3421701 3421901 Xkr4
mchr1   3648310 3648584 Xkr4
mchr1   3648584 3648859 Xkr4
mchr1   3648859 3649134 Xkr4
mchr1   3649134 3649409 Xkr4
mchr1   3649409 3649684 Xkr4
mchr1   3649684 3649959 Xkr4
mchr1   3649959 3650234 Xkr4
mchr1   3650234 3650509 Xkr4
mchr1   3658846 3658904 Xkr4
mchr1   3670551 3670787 Xkr4
mchr1   3670787 3671024 Xkr4
mchr1   3671024 3671261 Xkr4
mchr1   3671261 3671498 Xkr4
mchr1   4290845 4291115 Rp1
mchr1   4291115 4291386 Rp1
mchr1   4291386 4291657 Rp1
mchr1   4291657 4291928 Rp1
mchr1   4291928 4292199 Rp1
mchr1   4292199 4292470 Rp1
mchr1   4292470 4292741 Rp1

[igor]

Can you post your config file as well? I've seen this happen with certain config options.

[2nelly]

I solved this problem at the end. It was matter of chromosome nomenclature. I tried all possible combinations and I found the correct one. Just to inform everyone that has common problem, the sentence: "Your file must be in .BED format, and it must be sorted" is not an error, just a warning. Afterwards, you should get under this sentence the following one "Number of exons analysed in chromosome m6 : ". So if the number of analysed exons is 0, then something is wrong. If it s another random number, everything works like a charm.