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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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GCmodel not in /lib #51

Closed YannLeGuen closed 4 years ago

YannLeGuen commented 4 years ago

Hi,

I would like to run the detect_cnv.pl script and adjust by GCmodel, as in the example 3

$ perl runex.pl  3
Exercise 3: individual-based calling with GCmodel signal adjustment, write to ex3.rawcnv
    Running command <detect_cnv.pl -test -hmm example.hmm -pfb example.pfb -log ex3.log -out ex3.rawcnv -gcmodel ../lib/hh550.hg18.gcmodel -conf -list inputlist>

In the FAQ http://penncnv.openbioinformatics.org/en/latest/misc/faq/ it is written that

gcmodel files have been provided in the lib/ folder.

However, this is not the case. Could you clarify where I can find these GCmodel files for Illumina arrays. I found the ones for Affymetrix arrays at: http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz

Thanks, Yann

kaichop commented 4 years ago

You can build GC model for your array (the file differs for each array) by cal-gc-snp

On Jan 28, 2020, at 2:16 PM, YannLeGuen notifications@github.com wrote:

 Hi,

I would like to run the detect_cnv.pl script and adjust by GCmodel, as in the example 3

$ perl runex.pl 3 Exercise 3: individual-based calling with GCmodel signal adjustment, write to ex3.rawcnv Running command <detect_cnv.pl -test -hmm example.hmm -pfb example.pfb -log ex3.log -out ex3.rawcnv -gcmodel ../lib/hh550.hg18.gcmodel -conf -list inputlist> In the FAQ http://penncnv.openbioinformatics.org/en/latest/misc/faq/ it is written that

gcmodel files have been provided in the lib/ folder. However, this is not the case. Could you clarify where I can find these GCmodel files for Illumina arrays. I found the ones for Affymetrix arrays at: http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz

Thanks, Yann

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YannLeGuen commented 4 years ago

Thank you for the advice. This was also in the FAQ. Since I have data from an old Illumina platform, I was curious to compare it with the one that is apparently required to run the example 3 quoted above. It's ok if it is not available/distributed anymore.

YannLeGuen commented 4 years ago

Hi,

In this case, do you advise to build a gcmodel for each individual? and then adjust each individual signal with genomic_wave.pl? cal_gc_snp seems to take as input individual subject signal and not a file list as detect_cnv does..

Thanks

kaichop commented 4 years ago

gcmodel is for each array, not for each individual. It includes gc for each marker in the array. cal_gc_snp uses the input file because it has the information on the marker (chr, position).

On Tue, Jan 28, 2020 at 4:33 PM YannLeGuen notifications@github.com wrote:

Hi,

In this case, do you advise to build a gcmodel for each individual? and then adjust each individual signal with genomic_wave.pl? cal_gc_snp seems to take as input individual subject signal and not a file list as detect_cnv does..

Thanks

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YannLeGuen commented 4 years ago

I see thank you.