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mixoviz

Detection and visualization of 2n/3n mixoploidy from a VCF. This repo contains the scripts used to calculate ratios of diploid-triploid mixoploidy within a Whole Genome Sequencing (WGS) sample. The only input requirement is a tabix-indexed VCF file containing a trio (child, mother, father) with alleles depths (AD tag) and call quality (GQ tag). We have tested the scripts using VCF files from GATK3 on human samples.

Requirements

  1. Python - tested with Python 3.6.1
  2. matplotlib, numpy, PyVCF - available via pip install matplotlib numpy pyvcf
  3. tabix - part of htslib, all VCF inputs are expected as tabix-indexed VCF files

Available Scripts

For specific instructions on each script, run python3 <ScriptName.py> -h.

  1. BAllele.py - Generates a B-allele plot for each chromosome for a single sample (trio not required).
  2. TrioBAllele.py - Generates a 3x3 B-allele plot for each chromosome using trio information to deconvolute the variants.
  3. TrioMixoploid.py - Calculates the percentage of diploid and triploid cells present in a sample under the assumption that the source of the extra haplotype is the mother. Calculations are performed on individual chromosomes (i.e. mosaic trisomy) and across all autosomes (i.e. 2n/3n mixoploidy).

Reference

Pre-print on bioRxiv: Holt, James M. et al. Programmatic Detection of Diploid-Triploid Mixoploidy via Whole Genome Sequencing.