CNVkit intervarls questions
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Entering edit mode
22 months ago
emmanouil.a ▴ 110

Hi,

I have a Whole Exome Sequencing baits design of 84Mb.

Why I need to create an access file (access.hg38.bed) if I already have the bait file?

When I run target command

cnvkit.py target --annotate ${flat_file} --split ${baits_file} -o "hg38_baits_annot_split.bed"

the design now is 81Mb and not any more 84Mb, why?

When I run the autobin command

cnvkit.py autobin *.bam --annotate ${flat_file} -t ${baits_file} -g access.hg38.bed

I have the output

            Depth   Bin size
Target:     64.095  1560
Antitarget: 1.665   60046

In the above cnvkit.py target command I have to add the -a option with the value of 1560 ? or keep the deafult value off 266 considering that is a WES?

Many thanks

CNVkit • 495 views
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