help with germline analysis using cnvkit
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Entering edit mode
8 days ago
ww22runner ▴ 60

Hi all, my bio is not very strong so please excuse this basic questions. I am trying to process only germline samples in my run using cnvkit. Usually with paired samples, I run:

cnvkit.py batch *Tumor.bam --normal *Normal.bam \
    --targets my_baits.bed  \
    --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
    --output-reference my_reference.cnn --output-dir results/ \
    --diagram --scatter

with just germline samples I should run:

cnvkit.py batch --normal *Normal.bam \
    --targets my_baits.bed  \
    --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
    --output-reference my_reference.cnn --output-dir results/ \
    --diagram --scatter

and

cnvkit.py batch $CNV_BAMS/*_G.bam \       
 -r  $CNV_BAMS/my_reference.cnn  \ 
 -p 8 \
-d $CNV_G_RESULTS

right?

Also, cnvkit Version v0.9.7 beta suggests that after the batch step, we should call these commands: a) segmetrics b) call c) bintest d) cnv_ztest.py

Could someone help me understand in simple terms what each step post batch command means and what the outcome is for that step?

Thank you

cnvkit • 130 views
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