if using pool reference, does the paired control sample no longer used for analysing. can you share your command? I ran my command like this, but I do not find any criteria to find the noisy sample
firstly, I used the batch command to get all the control samples target.cnn and antitarget.cnn
# command 1
cnvkit.py batch Tumor.bam --normal Normal.bam \
--targets my_baits.bed --annotate refFlat.txt \
--fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
--output-reference my_reference.cnn --output-dir results/ \
--diagram --scatter
Secondly, I gather all the control samples target.cnn and antitarget.cnn to a empty directory,
# command 2
cnvkit.py reference *coverage.cnn -f ucsc.hg19.fa -o Reference.cnn
Thirdly, I can not find that the cnvkit support control sample and pool rference just like the gatk Mutect2. so I can just give the pool reference and ignoring this normal sample
# command 3
cnvkit.py batch Tumor.bam --normal Reference.cnn \
--targets my_baits.bed --annotate refFlat.txt \
--fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
--output-reference my_reference.cnn --output-dir results/ \
--diagram --scatter
thanks a lot, and looking forward to hear more experience with cnvkit about you
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linouhao •
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linouhao •
