1. • Xin-zhuan Su
• Sittiporn Pattaradilokrat
• Sethu Nair
• Yanwei Qi
• Gordon Bullen
NIH/ NIAID – Malaria
Functional Genomics Section • Sebastian Gurevich
McGill University
Funding:
National Institutes of Health
Canadian Institutes of Health Research
• Philip Awadalla
University of Montreal
https://github.com/parasite-genomics/Pipelines - 2.0 Coming in July 2014
zmartine@gmail.com
ComPar: Genome Assembly, Variant Mapping, and
Validation Pipelines
Martine Zilversmit
http://www.slideshare.net/zmartine1/com-par-25jun14
2. ComPar: Genome Assembly, Variant Mapping, and
Validation Pipelines
https://github.com/parasite-genomics/Pipelines
• BASH-scripted
pipelines
• Accurate variant
prediction
– SNPs
– Small indels
– Large indels
(>17bp)
– Focused regions of
extreme divergence
(35-70% amino acid
identity)
• In silico variant
validation
3. Parameters:
- Quality Metric and Cutoff
- Number of variants per cluster
- Maximum distance between variants within a cluster
- Maximum distance between smaller clusters to merge
into an HDR
Finding Highly Divergent Regions – HDR Program
VCF File
False Positive
Variants
True Positive
Variants
HDR File:
- Size of HDR
- Position of HDR
- Variants Contained
Python - Stand-alone interactive or pipelined