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CNVnator output filter

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!

cnv filter
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updated by ChrisJ • ChrisJ • written by zhang248 • zhang248

1 answer

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

• 0 views • link
written by ChrisJ • ChrisJ

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

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written by zhang248 • zhang248

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