Basically I followed this tutorial for calling germline CNV from whole exome data set. https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants
First, I have generated a cohort mode. Then, I have call CNV for a sample against the cohort.
I end up with two vcf files interval genotype, segment genotype. Also I have a denoise copy ratio as a tsv fromat for the sample.
Looking for del and dup for each interval or each segment is not convenient from vcf. This is because VCF file provides a detailed listing of the most likely copy-number call for each genomic interval included in the data set.
My query is how to visualise data in a figure. Should I plot denoise copy ratio as y axis against coordinate x axis? Or Should I used interval CN as y axis?
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