Hi there,
I am trying to use JISTIC tool to analyze CNV data. I did not properly understand how to make the ProbeLocationFile.
Let's say, I have segmented file from DNACopy. The output files look like:
==> TestSample1 <==
barcode chromosome start stop mark segmean
sampleS1 1 567331 569882 6 -2.3721
sampleS1 1 761847 905536 162 -0.1232
sampleS1 1 905636 3549990 2846 -0.0335
==> TestSample2 <==
barcode chromosome start stop mark segmean
sampleS1 1 761857 7854094 4700 -0.0742
sampleS1 1 7858583 7861350 8 -0.8358
sampleS1 1 7862937 11905939 3063 -0.0598
==> TestSample3 <==
barcode chromosome start stop mark segmean
sampleS1 1 569890 761867 2 -0.0945
sampleS1 1 761967 1231403 767 -0.6182
sampleS1 1 1231503 1233381 8 -0.1089
As, chr-start-end position in each file are different. How do we make the same region for all file. Because not all regions are present in all samples.
So, how to make "Probe location file"?
Could you please help me with this. Thank you for your time and consideration.
cheers
Chirag
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Chirag Nepal
You need to be using the data pre-DNAcopy segmentation. In the case of WGS, that'll usually be read depth in genomic windows and for exomes, that'll be depth in small sections of the covered regions (as output by something like Varscan exome CN calling). The locations of those windows are your probe location file, and your input data is the read depths or log2 ratios from each of the windows.
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Chris Miller
Thanks Chris!
OK, will try that.
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Chirag Nepal
Hi Chris,
I ended up using varscan (pre-DNA copy segmentation) and GISTIC (for population analysis).
ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm
Output from varscan
head P1.copynumber
chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content
chr1 567331 567430 100 38.3 6.1 -2.515 47.0
chr1 567431 567459 29 29.8 5.6 -2.270 41.4
chr1 567497 567596 100 151.1 18.6 -2.882 48.0
For (6) Seg.CN (log2() -1 of copy number)
So, should I use: Seg.CN = (log2(-2.515 )-1) (why there is -1). In my trial run, I used log2(-2.515), and so on for each line.
I guess, as you suggested, it does not make sense to use output from DNAcopy segmentation, which are basically only the significant hits.
Thanks for your suggestions!
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Chirag Nepal
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Just wants to make sure. Is it GISTIC you're asking about? If yes, I guess you're asking about marker file?
I was referring to JISTIC http://www.c2b2.columbia.edu/danapeerlab/html/jistic.html , which is meant to be like an upgrade to GISTIC. I plan to try both. But for now, got stuck with making probe location file.