Hey everyone
I am having a hard time dealing with CNVnator .. well the results it generates..
I have array data, exome-seq data which the CNV calls line up .... Now using WGS data and I am getting loads of calls (10,000s) from CNVnator but where I know there are CNVs (confirmed by taqman) I am not getting that called in CNVnator ...
My Pipe for WGS is bowtie2 -> Picard Mark dups -> GATK (base score and INDEL)
Appreciate any help as I have been stuck on this for weeks
Cheers
Josh
I am having a hard time dealing with CNVnator .. well the results it generates..
I have array data, exome-seq data which the CNV calls line up .... Now using WGS data and I am getting loads of calls (10,000s) from CNVnator but where I know there are CNVs (confirmed by taqman) I am not getting that called in CNVnator ...
My Pipe for WGS is bowtie2 -> Picard Mark dups -> GATK (base score and INDEL)
Appreciate any help as I have been stuck on this for weeks
Cheers
Josh
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