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rgcgithub / clamms

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
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creating QCs metrics file #15

Open thedam opened 6 years ago

thedam commented 6 years ago

Hi, In the section "Selecting reference panels using the k-d tree" you recommend to use Picard's metrices: GCDROPOUT, ATDROPOUT, MEANINSERTSIZE, ONBAITVSSELECTED, PCTPFUQREADS, PCTTARGETBASES10X, and PCTTARGETBASES50X (...). Also QC metrics should be normalized (...)

How exactly should I create and normalize such file? (to obtain similar format like you presented in "example_qcs.Rdata")

Thanks Damian

pd3 commented 6 years ago

I'd like to ask the same question. Any chance the description could be extended to show an example of the picard command and other commands used to generate such file?

tanlaboratory commented 4 years ago

https://broadinstitute.github.io/picard/picard-metric-definitions.html