PennCNV for PIG DATA

[micpp]

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]

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.

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On Wed, Apr 17, 2019 at 11:20 AM micpp ***@***.***> 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! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#41>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuNnmBjhx3z1VWHhSmPWJEsOR15O0ks5vhzu1gaJpZM4c1UhB> .