CNVnator output filter

Question

[zhang248]

Hi, I'm using CNVnator to call CNVs. I have 30 samples, and the "duplication" of all the outputs has no one with e-val1<0.05. This is my pipeline

1. cnvnator -root temp/${sample}.root -unique -tree $bam

2. cnvnator -root temp/${sample}.root -his $bin -d $dir

3. cnvnator -root temp/${sample}.root -stat $bin

4. cnvnator -root temp/${sample}.root -partition $bin

5. cnvnator -root temp/${sample}.root -call $bin > ${sample}_cnv.txt

Can anyone tell me why? Thanks!

Answer 1

[ChrisJ]

Did you use the parameter of eval 1 ？if it is ,it should be OK .

[zhang248]

Sorry to reply you so late. My output is ok, I just mixed the "normalized_RD" and "e-val1".