Script to display Uniparental Disomies (UPD) on ideograms, based on trio exome/genome vcf
## Requirements
bcftools to manage variants : https://github.com/samtools/bcftools
tagore to plot ideograms : https://github.com/jordanlab/tagore
./UPD_plotter.sh $vcf $ped $output_prefix
where :
-$vcf is a sorted indexed multi sample vcf (order of samples do not matter, can have more than three samples)
-$ped is a pedigree file with at least four columns trio_name, child_ID, father_ID, mother_ID separated by tabulations, using the same IDs as in multi_vcf
outputs ideograms as PNG and SVG files, where informative variants are colored:
-biparental contribution in green (displayed on the left chromatid)
-maternal uniparental contribution in pink (displayed on the right chromatid)
-paternal uniparental contribution in blue (displayed on the right chromatid)
Example on trio exome (first) and trio genome (second):
