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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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PennCNV for PIG DATA #41

Open micpp opened 5 years ago

micpp commented 5 years ago

Dear Dr. Wang, I used the PennCNV in my PIG DATA and I have some doubts. My SNP chip has 50,915 SNPs (GGP_Porcine_HD_E) from illumina plataform. Could you help me, please?

I used genomic_wave.pl for create my adjusted list. So I used the command bellow:

./detect_cnv.pl -test -hmm lib/hhall.hmm -pfb hernia_escrotal.pfb -confidence -minlength 1000 -log detect_cnv_com_minlength.log -list lista_adj.txt -out allsample_adjusted_com_minlength.rawcnv

My doubts are:

Do not I need use the -gcmodel for adjustment the signal file in the command above, right?

My hmm file is it correct? I used hhall.hmm file for cnv call.

Thank you so much!

kaichop commented 5 years ago

you do not need to use gcmodel. Given that there are only 50K markers, better not to use any gc adjustment. hhall should work okay.

On Wed, Apr 17, 2019 at 11:20 AM micpp notifications@github.com wrote:

Dear Dr. Wang, I used the PennCNV in my PIG DATA and I have some doubts. My SNP chip has 50,915 SNPs (GGP_Porcine_HD_E) from illumina plataform. Could you help me, please?

I used genomic_wave.pl for create my adjusted list. So I used the command bellow:

./detect_cnv.pl -test -hmm lib/hhall.hmm -pfb hernia_escrotal.pfb -confidence -minlength 1000 -log detect_cnv_com_minlength.log -list lista_adj.txt -out allsample_adjusted_com_minlength.rawcnv

My doubts are:

Do not I need use the -gcmodel for adjustment the signal file in the command above, right?

My hmm file is it correct? I used hhall.hmm file for cnv call.

Thank you so much!

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