cnvkit.sh

A short script to run cnvkit

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cnvkit.sh is a shell script to run CNVkit for exome-seq. The shell uses the files produced by exome_test.sh. It allows for recentering the baseline by the average log2ratio of a certain chromosome.
***Update***
The seg can be annotated by cytoband with multithreading.
Individual chromosomal scattergrams are plotted.

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2018-07-24

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hg38 package
hg38 version of the pipelines for whole exome sequencing: exome_test38.sh wole transcription sequencing: rna_test38.sh somatic calling: somatic38.sh SV detect: svdetect38.sh, meerkat38.sh cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh *** Mutect2 instead of haptotypecaller is used to call variants in DNA-seq.