My Career

• Zoology
• Pathogen transmission
• Pathogen genomics
• Office for National Statistics - data science campus

Improving Cancer mutation detection

ACCURACY

Image credit: Illumina

Variant Call Format (VCF) file specification

							##fileformat=VCFv4.3
							##fileDate=20090805
							##source=myImputationProgramV3.1
							##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
							##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
							##phasing=partial
							##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
							##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
							##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
							##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
							##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
							##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
							##FILTER=<ID=q10,Description="Quality below 10">
							##FILTER=<ID=s50,Description="Less than 50% of samples have data">
							##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
							##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
							##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
							##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
							#CHROM POS      ID         REF   ALT    QUAL  FILTER   INFO                             FORMAT       NA00001         NA00002          NA00003
							20     14370    rs6054257  G     A      29    PASS    NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ  0|0:48:1:51,51  1|0:48:8:51,51   1/1:43:5:.,.
							20     17330    .          T     A      3     q10     NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ  0|0:49:3:58,50  0|1:3:5:65,3     0/0:41:3
							20     1110696  rs6040355  A     G,T    67    PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ  1|2:21:6:23,27  2|1:2:0:18,2     2/2:35:4
							20     1230237  .          T     .      47    PASS    NS=3;DP=13;AA=T                   GT:GQ:DP:HQ  0|0:54:7:56,60  0|0:48:4:51,51   0/0:61:2
							20     1234567  microsat1  GTC   G,GTCT 50    PASS    NS=3;DP=9;AA=G                    GT:GQ:DP     0/1:35:4        0/2:17:2         1/1:40:3
						

Cattle, possums, and bTB in New Zealand

SAMPLING

Image credit: Wikimedia

Image credit: Wikimedia

Cattle, badgers, and bTB in Woodchester Park

REPRESENTATIVENESS

Mapping HIV in Côte d'Ivoire

ANONYMITY

Data source: Data for good

Reproducible data science

REPRODUCIBILITY

							{
								"title": "Cote d'Ivoire: High Resolution Population Density Maps + Demographic Estimates. Population and Youth (15-24)",
								"source": "Facebook",
								"url": "https://data.humdata.org/dataset/highresolutionpopulationdensitymaps-civ",
								"type": "tif/csv",
								"date-of-dataset": "01-07-2019",
								"date-accessed": "23-03-2020"
							  }
						

BE TRANSPARENT

Image credit: The Turing Way

BE OPEN

Image credit: The Turing Way

BE MORE THAN REPRODUCIBLE