More Related Content Similar to Com par 25jun14 Similar to Com par 25jun14 (20) Com par 25jun141. • 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
4. NumberofVariants
Position on “Chromosome”
Dye-Terminator Sequenced Variation – 50 basepair Sliding window
Comparing 2 Plasmodium Genomes
200
400
600
800
1000
1200
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1600
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5400
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5800
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6400
6600
6800
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7800
8000
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8400
8600
8800
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9200
9400
9600
0
2
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10
12
5. Predicted Variants – No filtering Based on Quality Metrics
NumberofVariants
Position on “Chromosome”
NumberofVariants
Position on “Chromosome”
Comparing 2 Plasmodium Genomes
200
400
600
800
1000
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6600
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7800
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8400
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9400
9600
0
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7800
8000
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8400
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9400
9600
0
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True Variants
Unfiltered Results
6. NumberofVariants
Position on “Chromosome”
NumberofVariants
Position on “Chromosome”
Comparing 2 Plasmodium Genomes
200
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5400
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6600
6800
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7400
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8400
8600
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9400
9600
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7800
8000
8200
8400
8600
8800
9000
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9600
0
2
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12
True Variants
Unfiltered Results
200
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8600
8800
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9200
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9600
0
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12
True Variants
Quality 30 Cutoff
Predicted Variants - Filtering Based on Quality Score ≥ 30 Cutoff
7. NumberofVariants
Position on “Chromosome”
NumberofVariants
Position on “Chromosome”
Comparing 2 Plasmodium Genomes
Filtering Based on Consensus Quality (FQ) ≤ -100 Cutoff
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6600
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7400
7600
7800
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8200
8400
8600
8800
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9600
0
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12
True Variants
Unfiltered Results
Quality 30 Cutoff
200
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9600
0
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12
True Variants
FQ −100 Cuttoff
8. NumberofVariants
Position on “Chromosome”
NumberofVariants
Position on “Chromosome”
Comparing 2 Plasmodium Genomes
Highly-Divergent Regions (HDRs)
200
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True Variants
Unfiltered Results
Quality 30 Cutoff
FQ −100 Cuttoff
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9600
0
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True Variants
Unfiltered Results
Quality 30 Cutoff
FQ −100 Cuttoff
9. NumberofVariants
Position on “Chromosome”
NumberofVariants
Position on “Chromosome”
Comparing 2 Plasmodium Genomes
200
400
600
800
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1200
1400
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2000
2200
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6600
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8400
8600
8800
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9200
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9600
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12
True Variants
Unfiltered Results
Quality 30 Cutoff
FQ −100 Cuttoff
Quality ≥ 30 Variants without Consensus Quality ≥ -100
Highly-Divergent Regions (HDRs)
200
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8000
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True Variants
Quality 30, No HDRs
10. Characteristics of Highly Divergent Regions
33X 44.4%
By265 55.6%
N67 66.7%
histone acetyltransferase GCN5, putative (GCN5)
RNA-binding protein NOB1, putative
Percent Identity
DNA repair protein, putative
33X 41.4%
By265 79.3%
N67 51.7%
Editor's Notes MAPPING, DEFINE!
DE NOVO, DEFINE!
SAY WHAT VARIANTS ARE Define highly divergent regions Define highly divergent regions Define highly divergent regions Define highly divergent regions Define highly divergent regions Define highly divergent regions