[dmacmillan]

No I currently do not, to save time. I will try it with the GEM file though. I'll let you know how it goes!

[dmacmillan]

Oh I forgot to ask about the circos format script. I plugged in my *ratios.txt file and got some output. But it does not look like circos format to me, how am I supposed to use the output given from this script?

[valeu]

If it looks like:

hs1 1631000 1731000 3.953692
hs1 1731000 1831000 3.953692
hs1 1831000 1931000 3.953692
hs1 1931000 2031000 3.953692

Circos will undestand it. You should add to the Circos config something like:

<plot>
show    = yes
type    = scatter
file = yourFile.CNP.circos.txt

glyph = rectangle
 glyph_size = 4
 fill_color = dgrey
 stroke_color = dgrey
 stroke_thickness = 1

min   = 0
max   = 6
#r0    = 0.7r
#r1    = 0.975r
r0    = 0.76r
r1    = 0.975r

background       = no
background_color = vvlgrey
background_stroke_color = black
background_stroke_thickness = 1

axis           = yes
axis_color     = lgrey
axis_thickness = 1
axis_spacing   = 1

<rules>

<rule>
importance   = 100
condition    = var(value) >= 6
value=6
glyph = rectangle
 glyph_size = 4
 fill_color = red
 stroke_color = red
 stroke_thickness = 1
</rule>

<rule>
importance   = 100
condition    = var(value) > 2.5 && var(value) < 6
glyph = rectangle
 glyph_size = 4
 fill_color = orange
 stroke_color = orange
 stroke_thickness = 1
</rule>

<rule>
importance   = 85
condition    = var(value) < 1.5
 glyph_size = 4
 fill_color = blue
 stroke_color = blue
 stroke_thickness = 1
</rule>

<rule>
show=0
importance   = 85
condition    = var(value) < 0
color = blue
</rule>
</rules>

</plot>

[bw.]

Calling CNA and BAF for exome seq data without a control

Hi, I'm trying to use FREEC to call CNA and BAF in some exome seq samples, but haven't been able to make it work. The tool ran fine on the chr19 test data.

The problems I'm seeing are
- the tool runs but doesn't generate any of the output files except mpileup.txt_sample.cpn
It exits with the error message:
..There is no control sample!!!
You have to use a matching control sample to get adequite results since GC-bias is not the only bias in targeted sequencing

- even the .cpn file doesn't seem right because it tries to call copy number outside the target regions I provided via the TruSeq_exome_targeted_regions.hg19.bed
and not surprisingly calls them all as 0 copy number.


I'm running the tool on a pileup generated using samtools v.0.1.12. I'm using the following config file:


[general]
chrLenFile=hg19.len

window = 3000
step = 1000
ploidy = 2

#breakPointThreshold = -.001

#GCcontentProfile = GC_profile.cnp

intercept=1
minMappabilityPerWindow = 0.7

outputDir = .

sex=XY
breakPointType=4

#degree=3
#coefficientOfVariation = 0.05
#gemMappabilityFile = /hg19/out76_hg19.gem

chrFiles = FREEC_Linux64/chromosomes/

[sample]

mateFile=mpileup.txt
#mateCopyNumberFile=mpileup.txt_sample.cpn

inputFormat = pileup
mateOrientation = FR

[control]

[BAF]

SNPfile = hg19_snp131.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5


[target]
captureRegions=TruSeq_exome_targeted_regions.hg19.bed

[valeu]

Hi, at this moment there is no option to run FREEC on exome-seq data without control sample. But since you are the second person who wants to do it, I will probably add this option soon.

[bw.]

That would really useful!
My backup was to use per-exon mean target coverage generated by Picard HS Metrics, with some added correction for %GC, but I'd rather use your tool.
Thanks,
-Ben

[bwt4383]

Display of CNV-data in IGV

Hi, I am struggling with displaying CNV data generated with freec in IGV. Can somebody give me some advice how to display CNVs in an inutitive way?

Thanks!

[valeu]

Hi!

I think I should right a script to create a .WIG file from _ratio.txt (http://www.broadinstitute.org/igv/WIG)

If you code in perl, you could do it yourself and share the script. Otherwise, I will do it when I have time

[bwt4383]

Thanks for your reply! It would be very helpful if you could implement a script for .WIG file creation!
:-)

[valeu]

Version 5.7 of Control-FREEC can now create BedGraph tracks on demand. Just set

[general]
BedGraphOutput=TRUE

This format is supported by the UCSC genome browser as well as IGV (http://www.broadinstitute.org/software/igv/bedgraph)

[monkeychild]

Hi

I am (slowly) trying to integrate Control-FREEC into a pipeline, and I was wondering if there's a way to generate a GC-content profile outside of running the whole thing once. Like maybe one of the already existing scripts could be called outside of freec first?

[valeu]

Hi,

I have not foreseen an option to create a GC-content profile outside of FREEC. But you could make a trick: something like providing a read file with 10 reads and setting a window size.

I will think about adding a separate function to calculate this profile.

[valeu]

Hi,

so now you can generate a GC-content profile independently from FREEC:

http://bioinfo-out.curie.fr/projects/freec/tutorial.html#GCP

[yuhao]

a unusual problem in FREEC

I meet an unusual problem when I run FREEC. If I provide a mateCopyNumberFile, and then qsub, it will run sucessfully, but in fact I normally don't have mateCopyNumberFile, but if I don't provide it, it can't run, the error message is:

sh:samtools:command not found

Error: FREEC was not able to extract reads from /database/chenxi/task/cancerProgram/pipline/bwa/BPMICS4/sortedbam/PD1W_XXL_BPMICS4_NoIndex_modified.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



I can't figure out what happens here. My parameters are absolutely correct, and I have samtools in my working directory and environmental PATH.

Can anyone give me some helps? I am not able to run FREEC because of this.

[valeu]

I think I know what happens. When you provide mateCopyNumberFile, FREEC does not try to read your .BAM file. When there is no mateCopyNumberFile available FREEC tries to read your file by calling "samtools" in the command line. And it seems that "samtools" does not point to anything.

I would suggest two solutions:

1. in the bash script that you qsub, add something like

   export PATH=$PATH:/pathToSamtools
   #check whether samtools exists
   samtools 2>samtools.usage.txt
   #run FREEC
   freec -conf myCofig.txt

1. transform you .BAM file to .SAM. Then, FREEC will not need samtools.

If you prefer, you can write to me directly to [email protected]